rs10964759

chr9-20925922-A-G

Variant summary

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

The NM_001375567.1(FOCAD):c.2962-379A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 152,266 control chromosomes in the GnomAD database, including 475 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 0.062 (475 hom., cov: 32)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOCAD	NM_001375567.1	c.2962-379A>G		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11	c.2962-379A>G		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5	c.2962-379A>G		intron_variant		1		P1
FOCAD	ENST00000605086.5	n.1432-379A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0616 AC: 9376 AN: 152148 Hom.: 470 Cov.: 32

Gnomad AFR AF: 0.0153

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0825

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0616 AC: 9380 AN: 152266 Hom.: 475 Cov.: 32 AF XY: 0.0636 AC XY: 4736 AN XY: 74462

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0825

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0700 Hom.: 570

Bravo AF: 0.0558

Asia WGS AF: 0.192 AC: 667 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.72
Dann	Benign	0.80

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: rs10964759; hg19: chr9-20925921;