rs3092685

Variant names:

• chr20-40955312-C-T
• rs3092685

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 0.447 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.665 AC: 27521 AN: 41412

American (AMR) AF: 0.328 AC: 5013 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2992 AN: 5150

South Asian (SAS) AF: 0.418 AC: 2011 AN: 4808

European-Finnish (FIN) AF: 0.281 AC: 2970 AN: 10566

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24738 AN: 67942

Other (OTH) AF: 0.412 AC: 866 AN: 2100

Alfa AF: 0.385 Hom.: 48610

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs3092685; hg19: chr20-39583952;