Genetic Variant FAM13A:c.2844-3dupT (chr4-88731430-T-TA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_014883.4(FAM13A):c.2844-3dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00282 in 1,546,570 control chromosomes in the GnomAD database, including 93 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 52 hom., cov: 32)

Exomes 𝑓: 0.0015 ( 41 hom. )

Consequence

FAM13A
NM_014883.4 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.801

Variant links:

Genes affected

FAM13A (HGNC:19367): (family with sequence similarity 13 member A) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Implicated in chronic obstructive pulmonary disease. [provided by Alliance of Genome Resources, Apr 2022]

FAM13A links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 4-88731430-T-TA is Benign according to our data. Variant chr4-88731430-T-TA is described in ClinVar as [Benign]. Clinvar id is 778157.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13A	NM_014883.4 link	c.2844-3dupT		splice_region_variant, intron_variant	Intron 22 of 23	ENST00000264344.10	NP_055698.2	O94988-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000264344.10 link	c.2844-3dupT		splice_region_variant, intron_variant	Intron 22 of 23	5	NM_014883.4	ENSP00000264344.5		O94988-4

Frequencies

GnomAD3 genomes

AF:

0.0149

AC:

2274

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0521

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00491

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.0110

GnomAD2 exomes

AF:

0.00399

AC:

931

AN:

233454

AF XY:

0.00276

show subpopulations

Gnomad AFR exome

AF:

0.0536

Gnomad AMR exome

AF:

0.00212

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000452

Gnomad OTH exome

AF:

0.00157

GnomAD4 exome

AF:

0.00150

AC:

2086

AN:

1394308

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

897

AN XY:

697416

show subpopulations

Gnomad4 AFR exome

AF:

0.0540

AC:

1717

AN:

31816

Gnomad4 AMR exome

AF:

0.00248

AC:

104

AN:

41952

Gnomad4 ASJ exome

AF:

0.00

AC:

AN:

25312

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

39360

Gnomad4 SAS exome

AF:

0.000132

AC:

AN:

83568

Gnomad4 FIN exome

AF:

0.00

AC:

AN:

41874

Gnomad4 NFE exome

AF:

0.0000263

AC:

AN:

1066642

Gnomad4 Remaining exome

AF:

0.00361

AC:

210

AN:

58168

Heterozygous variant carriers

178

267

356

445

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

108

162

216

270

<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:

0.0150

AC:

2280

AN:

152262

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

1090

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0521

AC:

0.0521475

AN:

0.0521475

Gnomad4 AMR

AF:

0.00490

AC:

0.00490324

AN:

0.00490324

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.000415

AC:

0.000414594

AN:

0.000414594

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.000147

AC:

0.000147016

AN:

0.000147016

Gnomad4 OTH

AF:

0.0109

AC:

0.0108902

AN:

0.0108902

Heterozygous variant carriers

106

213

319

426

532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

110

<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:

0.00624

Hom.:

Bravo

AF:

0.0168

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.000110

EpiControl

AF:

0.0000594

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 26, 2018

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

Mutation Taster

=97/3

polymorphism

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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