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

Variant summary

Our verdict is Benign. The variant received -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

Publications

9 publications found

Variant links:

Genes affected

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

FOCAD Gene-Disease associations (from GenCC):

liver disease, severe congenital
Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

FOCAD 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=-0.97).

BP6

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

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375567.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FOCAD	NM_001375567.1	MANE Select	c.2625+11G>A	intron	N/A	NP_001362496.1	Q5VW36
FOCAD	NM_017794.5		c.2625+11G>A	intron	N/A	NP_060264.4
FOCAD	NM_001375568.1		c.2520+11G>A	intron	N/A	NP_001362497.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FOCAD	ENST00000338382.11	TSL:5 MANE Select	c.2625+11G>A	intron	N/A	ENSP00000344307.6	Q5VW36
FOCAD	ENST00000380249.5	TSL:1	c.2625+11G>A	intron	N/A	ENSP00000369599.1	Q5VW36
FOCAD	ENST00000605086.5	TSL:1	n.1095+11G>A	intron	N/A

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

GnomAD2 exomes

AF:

0.588

AC:

109363

AN:

186028

AF XY:

0.586

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 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

African (AFR)

AF:

0.590

AC:

16538

AN:

28044

American (AMR)

AF:

0.736

AC:

20481

AN:

27836

Ashkenazi Jewish (ASJ)

AF:

0.515

AC:

11187

AN:

21710

East Asian (EAS)

AF:

0.545

AC:

18774

AN:

34456

South Asian (SAS)

AF:

0.610

AC:

35562

AN:

58270

European-Finnish (FIN)

AF:

0.594

AC:

28826

AN:

48560

Middle Eastern (MID)

AF:

0.642

AC:

3343

AN:

5208

European-Non Finnish (NFE)

AF:

0.576

AC:

597958

AN:

1038342

Other (OTH)

AF:

0.584

AC:

31197

AN:

53390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

14470

28940

43410

57880

72350

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17540

35080

52620

70160

87700

<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:

0.586

AC:

89006

AN:

151768

Hom.:

26281

Cov.:

AF XY:

0.588

AC XY:

43639

AN XY:

74154

show subpopulations

African (AFR)

AF:

0.585

AC:

24199

AN:

41370

American (AMR)

AF:

0.669

AC:

10199

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.514

AC:

1781

AN:

3466

East Asian (EAS)

AF:

0.527

AC:

2721

AN:

5164

South Asian (SAS)

AF:

0.616

AC:

2961

AN:

4806

European-Finnish (FIN)

AF:

0.600

AC:

6304

AN:

10510

Middle Eastern (MID)

AF:

0.639

AC:

188

AN:

294

European-Non Finnish (NFE)

AF:

0.572

AC:

38852

AN:

67900

Other (OTH)

AF:

0.584

AC:

1233

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1821

3643

5464

7286

9107

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<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:

0.542

Hom.:

7990

Bravo

AF:

0.592

Asia WGS

AF:

0.543

AC:

1886

AN:

3476

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.63

(source)

DANN

Benign

0.68

PhyloP100

-0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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

Computational scores

Splicing

Publications

Other links and lift over