20-3775950-T-C

Variant names:

• chr20-3775950-T-C
• rs13043330

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 0.61 in 152,074 control chromosomes in the GnomAD database, including 28,355 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 0.61 (28355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

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 (EAS) allele frequency at 95% confidence interval = 0.612 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: 0.610 AC: 92649 AN: 151956 Hom.: 28327 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.610 AC: 92741 AN: 152074 Hom.: 28355 Cov.: 32 AF XY: 0.609 AC XY: 45252 AN XY: 74338

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.575

Alfa AF: 0.604 Hom.: 54276

Bravo AF: 0.608

Asia WGS AF: 0.563 AC: 1956 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	2.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13043330; hg19: chr20-3756597; COSMIC: COSV65729585;