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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.782 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

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.794

Alfa AF: 0.782 Hom.: 10357

Bravo AF: 0.780

Asia WGS AF: 0.770 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2394953; hg19: chr6-31233353;