dbSNP rs7875153: FOCAD:c.907-49A>G (chr9-20778632-A-G) – 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.907-49A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 996,018 control chromosomes in the GnomAD database, including 364,082 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.84 ( 53699 hom., cov: 32)

Exomes 𝑓: 0.86 ( 310383 hom. )

Consequence

FOCAD
NM_001375567.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0820

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=-0.68).

BP6

Variant 9-20778632-A-G is Benign according to our data. Variant chr9-20778632-A-G is described in ClinVar as Benign. ClinVar VariationId is 1281513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.886 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.907-49A>G	intron	N/A	NP_001362496.1	Q5VW36
FOCAD	NM_017794.5		c.907-49A>G	intron	N/A	NP_060264.4
FOCAD	NM_001375568.1		c.907-49A>G	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.907-49A>G	intron	N/A	ENSP00000344307.6	Q5VW36
FOCAD	ENST00000380249.5	TSL:1	c.907-49A>G	intron	N/A	ENSP00000369599.1	Q5VW36
FOCAD	ENST00000894775.1		c.907-49A>G	intron	N/A	ENSP00000564834.1

Frequencies

GnomAD3 genomes

AF:

0.839

AC:

127618

AN:

152102

Hom.:

53667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.784

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.898

Gnomad ASJ

AF:

0.841

Gnomad EAS

AF:

0.773

Gnomad SAS

AF:

0.852

Gnomad FIN

AF:

0.891

Gnomad MID

AF:

0.873

Gnomad NFE

AF:

0.855

Gnomad OTH

AF:

0.856

GnomAD2 exomes

AF:

0.857

AC:

188778

AN:

220250

AF XY:

0.858

show subpopulations

Gnomad AFR exome

AF:

0.785

Gnomad AMR exome

AF:

0.939

Gnomad ASJ exome

AF:

0.830

Gnomad EAS exome

AF:

0.766

Gnomad FIN exome

AF:

0.887

Gnomad NFE exome

AF:

0.852

Gnomad OTH exome

AF:

0.869

GnomAD4 exome

AF:

0.857

AC:

723141

AN:

843796

Hom.:

310383

Cov.:

AF XY:

0.857

AC XY:

379572

AN XY:

442704

show subpopulations

African (AFR)

AF:

0.792

AC:

17337

AN:

21884

American (AMR)

AF:

0.934

AC:

38162

AN:

40874

Ashkenazi Jewish (ASJ)

AF:

0.838

AC:

18205

AN:

21722

East Asian (EAS)

AF:

0.812

AC:

29799

AN:

36712

South Asian (SAS)

AF:

0.861

AC:

60890

AN:

70754

European-Finnish (FIN)

AF:

0.886

AC:

44785

AN:

50558

Middle Eastern (MID)

AF:

0.896

AC:

4063

AN:

4534

European-Non Finnish (NFE)

AF:

0.854

AC:

476017

AN:

557072

Other (OTH)

AF:

0.854

AC:

33883

AN:

39686

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

4970

9940

14911

19881

24851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7134

14268

21402

28536

35670

<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:

0.839

AC:

127699

AN:

152222

Hom.:

53699

Cov.:

AF XY:

0.841

AC XY:

62621

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.783

AC:

32503

AN:

41496

American (AMR)

AF:

0.898

AC:

13739

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.841

AC:

2917

AN:

3470

East Asian (EAS)

AF:

0.773

AC:

4014

AN:

5192

South Asian (SAS)

AF:

0.852

AC:

4119

AN:

4832

European-Finnish (FIN)

AF:

0.891

AC:

9443

AN:

10604

Middle Eastern (MID)

AF:

0.881

AC:

259

AN:

294

European-Non Finnish (NFE)

AF:

0.855

AC:

58132

AN:

68012

Other (OTH)

AF:

0.850

AC:

1796

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1051

2102

3152

4203

5254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<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:

0.843

Hom.:

11109

Bravo

AF:

0.835

Asia WGS

AF:

0.783

AC:

2724

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

5.4

(source)

DANN

Benign

0.89

PhyloP100

0.082

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

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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

Computational scores

Splicing

Publications

Other links and lift over