rs3761243

Variant names:

• chr20-3042376-A-C
• rs3761243

Your query was ambiguous. Multiple possible variants found:

• chr20-3042376-A-C
• chr20-3042376-A-G
• chr20-3042376-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;