rs7631734

Variant names:

• chr3-138252065-G-A
• rs7631734
• NM_001363941.2:c.1134+6882G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-138252065-G-A
• chr3-138252065-G-C
• chr3-138252065-G-T

Variant summary

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

The NM_001363941.2(ARMC8):​c.1134+6882G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,022 control chromosomes in the GnomAD database, including 18,972 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 0.47 (18972 hom., cov: 32)
• Consequence: ARMC8 NM_001363941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 5 publications found

Genes affected

ARMC8 (HGNC:24999): (armadillo repeat containing 8) Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Located in cytosol and nucleoplasm. Part of ubiquitin ligase complex. [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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMC8	NM_001363941.2	c.1134+6882G>A		intron_variant	Intron 12 of 21	ENST00000469044.6	NP_001350870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMC8	ENST00000469044.6	c.1134+6882G>A		intron_variant	Intron 12 of 21	5	NM_001363941.2	ENSP00000419413.1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71036 AN: 151904 Hom.: 18966 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.467 AC: 71063 AN: 152022 Hom.: 18972 Cov.: 32 AF XY: 0.476 AC XY: 35375 AN XY: 74294

African (AFR) AF: 0.209 AC: 8657 AN: 41464

American (AMR) AF: 0.594 AC: 9079 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1840 AN: 3464

East Asian (EAS) AF: 0.840 AC: 4345 AN: 5174

South Asian (SAS) AF: 0.544 AC: 2619 AN: 4812

European-Finnish (FIN) AF: 0.617 AC: 6519 AN: 10560

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36431 AN: 67956

Other (OTH) AF: 0.482 AC: 1020 AN: 2114

Alfa AF: 0.517 Hom.: 66653

Bravo AF: 0.460

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.3
DANN	Benign	0.75
PhyloP100		0.53
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: rs7631734; hg19: chr3-137970907;