rs61670327

Variant names:

• chr5-3276582-G-A
• rs61670327

Your query was ambiguous. Multiple possible variants found:

• chr5-3276582-G-A
• chr5-3276582-G-C

Variant summary

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

The variant allele was found at a frequency of 0.547 in 151,678 control chromosomes in the GnomAD database, including 22,713 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 0.55 (22713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82913 AN: 151558 Hom.: 22689 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.547 AC: 82968 AN: 151678 Hom.: 22713 Cov.: 32 AF XY: 0.548 AC XY: 40584 AN XY: 74106

African (AFR) AF: 0.566 AC: 23407 AN: 41338

American (AMR) AF: 0.587 AC: 8958 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2143 AN: 3458

East Asian (EAS) AF: 0.537 AC: 2740 AN: 5106

South Asian (SAS) AF: 0.452 AC: 2170 AN: 4806

European-Finnish (FIN) AF: 0.585 AC: 6189 AN: 10582

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35581 AN: 67830

Other (OTH) AF: 0.578 AC: 1218 AN: 2106

Alfa AF: 0.539 Hom.: 2746

Bravo AF: 0.550

Asia WGS AF: 0.499 AC: 1736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.38
PhyloP100		-0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs61670327; hg19: chr5-3276696;