rs2844670

Variant names:

• chr6-31037949-G-A
• rs2844670

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.870 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

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.885

Alfa AF: 0.846 Hom.: 77401

Bravo AF: 0.879

Asia WGS AF: 0.825 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844670; hg19: chr6-31005726;