rs3092685

Variant names:

• chr20-40955312-C-T
• rs3092685

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 0.447 in 151,920 control chromosomes in the GnomAD database, including 16,629 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 0.45 (16629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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: 0.447 AC: 67784 AN: 151800 Hom.: 16601 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.447 AC: 67857 AN: 151920 Hom.: 16629 Cov.: 31 AF XY: 0.440 AC XY: 32683 AN XY: 74268

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.412

Alfa AF: 0.374 Hom.: 21624

Bravo AF: 0.458

Asia WGS AF: 0.487 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3092685; hg19: chr20-39583952;