rs7647266

Positions:

• chr3-122393534-T-C

Variant summary

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

The NM_014367.4(FAM162A):​c.35-9226T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,964 control chromosomes in the GnomAD database, including 27,383 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 0.60 (27383 hom., cov: 32)
• Consequence: FAM162A NM_014367.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

Genes affected

FAM162A (HGNC:17865): (family with sequence similarity 162 member A) Involved in several processes, including activation of cysteine-type endopeptidase activity involved in apoptotic process; cellular response to hypoxia; and positive regulation of release of cytochrome c from mitochondria. Located in cytosol and mitochondrion. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM162A	NM_014367.4	c.35-9226T>C		intron_variant		ENST00000477892.5	NP_055182.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM162A	ENST00000477892.5	c.35-9226T>C		intron_variant		1	NM_014367.4	ENSP00000419088	P1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90807 AN: 151846 Hom.: 27377 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.598 AC: 90855 AN: 151964 Hom.: 27383 Cov.: 32 AF XY: 0.597 AC XY: 44365 AN XY: 74256

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.606

Alfa AF: 0.592 Hom.: 12210

Bravo AF: 0.592

Asia WGS AF: 0.644 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.65

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: rs7647266; hg19: chr3-122112381; COSMIC: COSV51659079;