rs2853934

Variant names:

• chr6-31286151-A-T
• rs2853934

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 0.103 in 152,284 control chromosomes in the GnomAD database, including 907 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 0.10 (907 hom., cov: 33)
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 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: 0.103 AC: 15702 AN: 152166 Hom.: 908 Cov.: 33

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.103 AC: 15699 AN: 152284 Hom.: 907 Cov.: 33 AF XY: 0.0977 AC XY: 7278 AN XY: 74458

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.114

Alfa AF: 0.105 Hom.: 119

Bravo AF: 0.108

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853934; hg19: chr6-31253928;