rs2248902

Variant names:

• chr6-31266337-G-A
• rs2248902

Your query was ambiguous. Multiple possible variants found:

• chr6-31266337-G-A
• chr6-31266337-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 151,940 control chromosomes in the GnomAD database, including 3,266 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 (3266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

Selected	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: 29876 AN: 151822 Hom.: 3266 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.269

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: 29879 AN: 151940 Hom.: 3266 Cov.: 32 AF XY: 0.192 AC XY: 14275 AN XY: 74286

African (AFR) AF: 0.130 AC: 5407 AN: 41436

American (AMR) AF: 0.146 AC: 2228 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3472

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5182

South Asian (SAS) AF: 0.181 AC: 873 AN: 4818

European-Finnish (FIN) AF: 0.175 AC: 1851 AN: 10550

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17185 AN: 67880

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.197 Hom.: 828

Bravo AF: 0.191

Asia WGS AF: 0.116 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs2248902; hg19: chr6-31234114;