rs2394953

chr6-31265576-G-Achr6-31265576-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;