rs3761243

chr20-3042376-A-Cchr20-3042376-A-Gchr20-3042376-A-T

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 0.332 in 152,014 control chromosomes in the GnomAD database, including 8,576 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 0.33 (8576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 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: 0.332 AC: 50473 AN: 151894 Hom.: 8555 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.332 AC: 50541 AN: 152014 Hom.: 8576 Cov.: 32 AF XY: 0.334 AC XY: 24805 AN XY: 74306

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.312

Alfa AF: 0.332 Hom.: 1216

Bravo AF: 0.337

Asia WGS AF: 0.424 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
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: rs3761243; hg19: chr20-3023022;