dbSNP rs2383156: FOCAD:c.2625+11G>A (chr9-20885241-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_001375567.1(FOCAD):c.2625+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,467,584 control chromosomes in the GnomAD database, including 248,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 26281 hom., cov: 31)

Exomes 𝑓: 0.58 ( 222686 hom. )

Consequence

FOCAD
NM_001375567.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.797

Variant links:

Genes affected

FOCAD (HGNC:23377): (focadhesin) Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

FOCAD 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=-0.97).

BP6

Variant 9-20885241-G-A is Benign according to our data. Variant chr9-20885241-G-A is described in ClinVar as [Benign]. Clinvar id is 402872.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-20885241-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOCAD	NM_001375567.1 link	c.2625+11G>A		intron_variant	Intron 21 of 43	ENST00000338382.11	NP_001362496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOCAD	ENST00000338382.11 link	c.2625+11G>A		intron_variant	Intron 21 of 43	5	NM_001375567.1	ENSP00000344307.6		Q5VW36

Frequencies

GnomAD3 genomes

AF:

0.587

AC:

88972

AN:

151650

Hom.:

26277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.586

Gnomad AMI

AF:

0.623

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.527

Gnomad SAS

AF:

0.617

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.572

Gnomad OTH

AF:

0.588

GnomAD3 exomes

AF:

0.588

AC:

109363

AN:

186028

Hom.:

32541

AF XY:

0.586

AC XY:

59924

AN XY:

102192

show subpopulations

Gnomad AFR exome

AF:

0.586

Gnomad AMR exome

AF:

0.762

Gnomad ASJ exome

AF:

0.517

Gnomad EAS exome

AF:

0.503

Gnomad SAS exome

AF:

0.612

Gnomad FIN exome

AF:

0.591

Gnomad NFE exome

AF:

0.563

Gnomad OTH exome

AF:

0.590

GnomAD4 exome

AF:

0.581

AC:

763866

AN:

1315816

Hom.:

222686

Cov.:

AF XY:

0.581

AC XY:

377470

AN XY:

649482

show subpopulations

Gnomad4 AFR exome

AF:

0.590

Gnomad4 AMR exome

AF:

0.736

Gnomad4 ASJ exome

AF:

0.515

Gnomad4 EAS exome

AF:

0.545

Gnomad4 SAS exome

AF:

0.610

Gnomad4 FIN exome

AF:

0.594

Gnomad4 NFE exome

AF:

0.576

Gnomad4 OTH exome

AF:

0.584

GnomAD4 genome

AF:

0.586

AC:

89006

AN:

151768

Hom.:

26281

Cov.:

AF XY:

0.588

AC XY:

43639

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.585

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.514

Gnomad4 EAS

AF:

0.527

Gnomad4 SAS

AF:

0.616

Gnomad4 FIN

AF:

0.600

Gnomad4 NFE

AF:

0.572

Gnomad4 OTH

AF:

0.584

Alfa

AF:

0.542

Hom.:

7864

Bravo

AF:

0.592

Asia WGS

AF:

0.543

AC:

1886

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jun 14, 2019

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

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.63

DANN

Benign

0.68

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