rs2844670

Variant names:

• chr6-31037949-G-A
• rs2844670

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 0.87 in 152,196 control chromosomes in the GnomAD database, including 57,871 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 0.87 (57871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 36 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 (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132290 AN: 152078 Hom.: 57810 Cov.: 32

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.870 AC: 132409 AN: 152196 Hom.: 57871 Cov.: 32 AF XY: 0.870 AC XY: 64695 AN XY: 74398

African (AFR) AF: 0.940 AC: 39063 AN: 41548

American (AMR) AF: 0.891 AC: 13624 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3286 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3526 AN: 5170

South Asian (SAS) AF: 0.870 AC: 4185 AN: 4812

European-Finnish (FIN) AF: 0.837 AC: 8860 AN: 10586

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56960 AN: 68000

Other (OTH) AF: 0.885 AC: 1864 AN: 2106

Alfa AF: 0.852 Hom.: 206446

Bravo AF: 0.879

Asia WGS AF: 0.825 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.89
DANN	Benign	0.33
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2844670; hg19: chr6-31005726;