rs11603538

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_031471.6(FERMT3):c.787-10C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,573,828 control chromosomes in the GnomAD database, including 95,407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 8621 hom., cov: 33)

Exomes 𝑓: 0.35 ( 86786 hom. )

Consequence

FERMT3
NM_031471.6 intron

Scores

Splicing: ADA: 0.00009313

Clinical Significance

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

Conservation

PhyloP100: -3.52

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 11-64219241-C-A is Benign according to our data. Variant chr11-64219241-C-A is described in ClinVar as [Benign]. Clinvar id is 402862.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64219241-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FERMT3	NM_031471.6 link	c.787-10C>A		intron_variant	Intron 6 of 14	ENST00000345728.10	NP_113659.3	Q86UX7-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FERMT3	ENST00000345728.10 link	c.787-10C>A		intron_variant	Intron 6 of 14	1	NM_031471.6	ENSP00000339950.5		Q86UX7-2

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50641

AN:

151968

Hom.:

8605

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.398

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.334

GnomAD3 exomes

AF:

0.328

AC:

61757

AN:

188526

Hom.:

10308

AF XY:

0.324

AC XY:

32851

AN XY:

101388

show subpopulations

Gnomad AFR exome

AF:

0.303

Gnomad AMR exome

AF:

0.404

Gnomad ASJ exome

AF:

0.262

Gnomad EAS exome

AF:

0.279

Gnomad SAS exome

AF:

0.271

Gnomad FIN exome

AF:

0.301

Gnomad NFE exome

AF:

0.343

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.348

AC:

494079

AN:

1421740

Hom.:

86786

Cov.:

AF XY:

0.345

AC XY:

242592

AN XY:

703964

show subpopulations

Gnomad4 AFR exome

AF:

0.307

Gnomad4 AMR exome

AF:

0.410

Gnomad4 ASJ exome

AF:

0.260

Gnomad4 EAS exome

AF:

0.315

Gnomad4 SAS exome

AF:

0.273

Gnomad4 FIN exome

AF:

0.304

Gnomad4 NFE exome

AF:

0.358

Gnomad4 OTH exome

AF:

0.342

GnomAD4 genome

AF:

0.333

AC:

50694

AN:

152088

Hom.:

8621

Cov.:

AF XY:

0.331

AC XY:

24621

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.307

Gnomad4 AMR

AF:

0.398

Gnomad4 ASJ

AF:

0.262

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.278

Gnomad4 FIN

AF:

0.296

Gnomad4 NFE

AF:

0.352

Gnomad4 OTH

AF:

0.339

Alfa

AF:

0.332

Hom.:

3055

Bravo

AF:

0.340

Asia WGS

AF:

0.336

AC:

1166

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.011

DANN

Benign

0.61

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000093

dbscSNV1_RF

Benign

0.034

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over