rs4977831

Variant names:

• chr9-20713069-A-G
• rs4977831
• NM_001375567.1:c.-32-2253A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-20713069-A-G
• chr9-20713069-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375567.1(FOCAD):​c.-32-2253A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,150 control chromosomes in the GnomAD database, including 66,834 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.94 (66834 hom., cov: 30)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 5 publications found

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOCAD	NM_001375567.1	MANE Select	c.-32-2253A>G		intron	N/A	NP_001362496.1	Q5VW36
	FOCAD	NM_017794.5		c.-32-2253A>G		intron	N/A	NP_060264.4
	FOCAD	NM_001375568.1		c.-32-2253A>G		intron	N/A	NP_001362497.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOCAD	ENST00000338382.11	TSL:5 MANE Select	c.-32-2253A>G		intron	N/A	ENSP00000344307.6	Q5VW36
	FOCAD	ENST00000380249.5	TSL:1	c.-32-2253A>G		intron	N/A	ENSP00000369599.1	Q5VW36
	FOCAD	ENST00000894775.1		c.-32-2253A>G		intron	N/A	ENSP00000564834.1

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142249 AN: 152030 Hom.: 66769 Cov.: 30

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.949

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.936 AC: 142367 AN: 152150 Hom.: 66834 Cov.: 30 AF XY: 0.935 AC XY: 69530 AN XY: 74368

African (AFR) AF: 0.984 AC: 40869 AN: 41538

American (AMR) AF: 0.950 AC: 14534 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3708 AN: 5118

South Asian (SAS) AF: 0.890 AC: 4292 AN: 4822

European-Finnish (FIN) AF: 0.945 AC: 10009 AN: 10590

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62471 AN: 67992

Other (OTH) AF: 0.941 AC: 1991 AN: 2116

Alfa AF: 0.920 Hom.: 32584

Bravo AF: 0.939

Asia WGS AF: 0.801 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.40
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4977831; hg19: chr9-20713068;