chr3-122408942-C-T

Variant names:

• chr3-122408942-C-T
• rs10511409
• NM_014367.4:c.373-797C>T

Variant summary

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

The NM_014367.4(FAM162A):​c.373-797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,882 control chromosomes in the GnomAD database, including 7,526 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 0.31 (7526 hom., cov: 31)
• Consequence: FAM162A NM_014367.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 11 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM162A	NM_014367.4	c.373-797C>T		intron_variant	Intron 4 of 4	ENST00000477892.5	NP_055182.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM162A	ENST00000477892.5	c.373-797C>T		intron_variant	Intron 4 of 4	1	NM_014367.4	ENSP00000419088.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47602 AN: 151764 Hom.: 7523 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.314 AC: 47631 AN: 151882 Hom.: 7526 Cov.: 31 AF XY: 0.317 AC XY: 23549 AN XY: 74220

African (AFR) AF: 0.342 AC: 14141 AN: 41376

American (AMR) AF: 0.276 AC: 4214 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3466

East Asian (EAS) AF: 0.275 AC: 1418 AN: 5162

South Asian (SAS) AF: 0.319 AC: 1537 AN: 4820

European-Finnish (FIN) AF: 0.356 AC: 3728 AN: 10484

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20381 AN: 67988

Other (OTH) AF: 0.313 AC: 662 AN: 2114

Alfa AF: 0.305 Hom.: 10880

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		-0.12
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: rs10511409; hg19: chr3-122127789;