chr11-64210595-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_031471.6(FERMT3):c.161-16C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,610,436 control chromosomes in the GnomAD database, including 18,988 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1165 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17823 hom. )

Consequence

FERMT3
NM_031471.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0890

Publications

8 publications found

Variant links:

Genes affected

FERMT3 (HGNC:23151): (FERM domain containing kindlin 3) Kindlins are a small family of proteins that mediate protein-protein interactions involved in integrin activation and thereby have a role in cell adhesion, migration, differentiation, and proliferation. The protein encoded by this gene has a key role in the regulation of hemostasis and thrombosis. This protein may also help maintain the membrane skeleton of erythrocytes. Mutations in this gene cause the autosomal recessive leukocyte adhesion deficiency syndrome-III (LAD-III). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2010]

FERMT3 Gene-Disease associations (from GenCC):

leukocyte adhesion deficiency 3
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet, ClinGen

FERMT3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-64210595-C-G is Benign according to our data. Variant chr11-64210595-C-G is described in ClinVar as Benign. ClinVar VariationId is 402861.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031471.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FERMT3	NM_031471.6	MANE Select	c.161-16C>G	intron	N/A	NP_113659.3
FERMT3	NM_001382362.1		c.161-16C>G	intron	N/A	NP_001369291.1
FERMT3	NM_178443.3		c.161-16C>G	intron	N/A	NP_848537.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FERMT3	ENST00000345728.10	TSL:1 MANE Select	c.161-16C>G	intron	N/A	ENSP00000339950.5
FERMT3	ENST00000279227.10	TSL:1	c.161-16C>G	intron	N/A	ENSP00000279227.5
FERMT3	ENST00000698855.1		n.1797C>G	non_coding_transcript_exon	Exon 1 of 13

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16843

AN:

152010

Hom.:

1165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0439

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.0893

Gnomad ASJ

AF:

0.0761

Gnomad EAS

AF:

0.0961

Gnomad SAS

AF:

0.0761

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.101

GnomAD2 exomes

AF:

0.117

AC:

29230

AN:

249182

AF XY:

0.119

show subpopulations

Gnomad AFR exome

AF:

0.0426

Gnomad AMR exome

AF:

0.0850

Gnomad ASJ exome

AF:

0.0716

Gnomad EAS exome

AF:

0.0875

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.158

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.151

AC:

220596

AN:

1458308

Hom.:

17823

Cov.:

AF XY:

0.149

AC XY:

107960

AN XY:

725168

show subpopulations

African (AFR)

AF:

0.0395

AC:

1319

AN:

33402

American (AMR)

AF:

0.0858

AC:

3832

AN:

44678

Ashkenazi Jewish (ASJ)

AF:

0.0709

AC:

1849

AN:

26082

East Asian (EAS)

AF:

0.128

AC:

5059

AN:

39642

South Asian (SAS)

AF:

0.0750

AC:

6468

AN:

86204

European-Finnish (FIN)

AF:

0.127

AC:

6784

AN:

53366

Middle Eastern (MID)

AF:

0.0584

AC:

336

AN:

5754

European-Non Finnish (NFE)

AF:

0.169

AC:

187089

AN:

1108988

Other (OTH)

AF:

0.131

AC:

7860

AN:

60192

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

10346

20692

31038

41384

51730

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6612

13224

19836

26448

33060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.111

AC:

16850

AN:

152128

Hom.:

1165

Cov.:

AF XY:

0.108

AC XY:

8021

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0440

AC:

1828

AN:

41514

American (AMR)

AF:

0.0894

AC:

1366

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0761

AC:

264

AN:

3468

East Asian (EAS)

AF:

0.0959

AC:

495

AN:

5162

South Asian (SAS)

AF:

0.0766

AC:

370

AN:

4830

European-Finnish (FIN)

AF:

0.114

AC:

1203

AN:

10596

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10959

AN:

67952

Other (OTH)

AF:

0.0999

AC:

211

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

765

1529

2294

3058

3823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0778

Hom.:

125

Bravo

AF:

0.107

Asia WGS

AF:

0.0850

AC:

294

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 11, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency

Leukocyte adhesion deficiency 3

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.2

(source)

DANN

Benign

0.35

PhyloP100

-0.089

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over