rs4977831

chr9-20713069-A-Gchr9-20713069-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOCAD	NM_001375567.1	c.-32-2253A>G		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11	c.-32-2253A>G		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5	c.-32-2253A>G		intron_variant		1		P1

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

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.941

Alfa AF: 0.919 Hom.: 29289

Bravo AF: 0.939

Asia WGS AF: 0.801 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.29
Dann	Benign	0.40

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

Other links and lift over

dbSNP: rs4977831; hg19: chr9-20713068;