rs2844494

Variant names:

• chr6-31515638-C-A
• rs2844494

Your query was ambiguous. Multiple possible variants found:

• chr6-31515638-C-A
• chr6-31515638-C-G
• chr6-31515638-C-T

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 0.699 in 152,064 control chromosomes in the GnomAD database, including 37,346 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 0.70 (37346 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.699 AC: 106267 AN: 151946 Hom.: 37317 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.699 AC: 106344 AN: 152064 Hom.: 37346 Cov.: 31 AF XY: 0.703 AC XY: 52230 AN XY: 74324

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.696

Alfa AF: 0.681 Hom.: 49204

Bravo AF: 0.690

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844494; hg19: chr6-31483415;