rs1612904

Variant names:

• chr6-32701241-C-A
• rs1612904

Your query was ambiguous. Multiple possible variants found:

• chr6-32701241-C-A
• chr6-32701241-C-G
• chr6-32701241-C-T

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 0.67 in 151,928 control chromosomes in the GnomAD database, including 34,579 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 0.67 (34579 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.670 AC: 101711 AN: 151810 Hom.: 34553 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.670 AC: 101787 AN: 151928 Hom.: 34579 Cov.: 31 AF XY: 0.674 AC XY: 50055 AN XY: 74248

African (AFR) AF: 0.651 AC: 26960 AN: 41390

American (AMR) AF: 0.759 AC: 11597 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2748 AN: 3468

East Asian (EAS) AF: 0.858 AC: 4435 AN: 5166

South Asian (SAS) AF: 0.763 AC: 3674 AN: 4818

European-Finnish (FIN) AF: 0.665 AC: 7014 AN: 10544

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42910 AN: 67960

Other (OTH) AF: 0.716 AC: 1510 AN: 2108

Alfa AF: 0.647 Hom.: 90411

Bravo AF: 0.679

Asia WGS AF: 0.834 AC: 2902 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.14
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1612904; hg19: chr6-32669018;