9-20739883-A-G

Variant names:

• chr9-20739883-A-G
• rs4446809
• NM_001375567.1:c.288-353A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375567.1(FOCAD):​c.288-353A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,088 control chromosomes in the GnomAD database, including 49,699 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 0.81 (49699 hom., cov: 32)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOCAD	NM_001375567.1	c.288-353A>G		intron_variant	Intron 4 of 43	ENST00000338382.11	NP_001362496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOCAD	ENST00000338382.11	c.288-353A>G		intron_variant	Intron 4 of 43	5	NM_001375567.1	ENSP00000344307.6
FOCAD	ENST00000380249.5	c.288-353A>G		intron_variant	Intron 6 of 45	1		ENSP00000369599.1
FOCAD	ENST00000604103.1	n.83-353A>G		intron_variant	Intron 1 of 4	4
FOCAD	ENST00000605031.5	n.64-353A>G		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122522 AN: 151970 Hom.: 49669 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.806 AC: 122601 AN: 152088 Hom.: 49699 Cov.: 32 AF XY: 0.809 AC XY: 60130 AN XY: 74342

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.821

Alfa AF: 0.822 Hom.: 19678

Bravo AF: 0.800

Asia WGS AF: 0.780 AC: 2711 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.8
DANN	Benign	0.64

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: rs4446809; hg19: chr9-20739882;