rs2853953

Variant names:

• chr6-31267728-G-A
• rs2853953

Your query was ambiguous. Multiple possible variants found:

• chr6-31267728-G-A
• chr6-31267728-G-C
• chr6-31267728-G-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 0.197 in 151,242 control chromosomes in the GnomAD database, including 3,258 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 0.20 (3258 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.197 AC: 29824 AN: 151124 Hom.: 3258 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.197 AC: 29827 AN: 151242 Hom.: 3258 Cov.: 31 AF XY: 0.193 AC XY: 14242 AN XY: 73886

African (AFR) AF: 0.131 AC: 5392 AN: 41024

American (AMR) AF: 0.146 AC: 2223 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3464

East Asian (EAS) AF: 0.0525 AC: 271 AN: 5164

South Asian (SAS) AF: 0.181 AC: 870 AN: 4810

European-Finnish (FIN) AF: 0.176 AC: 1845 AN: 10478

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.253 AC: 17167 AN: 67770

Other (OTH) AF: 0.193 AC: 404 AN: 2094

Alfa AF: 0.225 Hom.: 5988

Bravo AF: 0.191

Asia WGS AF: 0.116 AC: 404 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.44
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs2853953; hg19: chr6-31235505;