rs2394953

Variant names:

• chr6-31265576-G-A
• rs2394953

Your query was ambiguous. Multiple possible variants found:

• chr6-31265576-G-A
• chr6-31265576-G-C

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 0.782 in 151,982 control chromosomes in the GnomAD database, including 46,407 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 0.78 (46407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 13 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 (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.782 AC: 118699 AN: 151866 Hom.: 46373 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.782 AC: 118779 AN: 151982 Hom.: 46407 Cov.: 32 AF XY: 0.781 AC XY: 58039 AN XY: 74280

African (AFR) AF: 0.765 AC: 31655 AN: 41358

American (AMR) AF: 0.780 AC: 11929 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3064 AN: 3466

East Asian (EAS) AF: 0.820 AC: 4252 AN: 5184

South Asian (SAS) AF: 0.756 AC: 3644 AN: 4818

European-Finnish (FIN) AF: 0.789 AC: 8326 AN: 10550

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53268 AN: 68014

Other (OTH) AF: 0.794 AC: 1671 AN: 2104

Alfa AF: 0.793 Hom.: 31239

Bravo AF: 0.780

Asia WGS AF: 0.770 AC: 2682 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	4.8
DANN	Benign	0.15
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2394953; hg19: chr6-31233353;