rs6788377

chr3-122387538-G-Achr3-122387538-G-Cchr3-122387538-G-T

Variant summary

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

The NM_014367.4(FAM162A):c.34+3239G>A 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 152,080 control chromosomes in the GnomAD database, including 27,405 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 (27405 hom., cov: 32)
• Consequence: FAM162A NM_014367.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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=-0.94).
• 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	UniProt
FAM162A	NM_014367.4	c.34+3239G>A		intron_variant		ENST00000477892.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM162A	ENST00000477892.5	c.34+3239G>A		intron_variant		1	NM_014367.4	P1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90871 AN: 151962 Hom.: 27399 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.634

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: 90919 AN: 152080 Hom.: 27405 Cov.: 32 AF XY: 0.597 AC XY: 44395 AN XY: 74334

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.607

Alfa AF: 0.573 Hom.: 10168

Bravo AF: 0.592

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.0050
Dann	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs6788377; hg19: chr3-122106385;