rs3843776

Variant names:

• chr20-24009015-G-A
• rs3843776

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 0.234 in 152,098 control chromosomes in the GnomAD database, including 8,686 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 0.23 (8686 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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: 0.233 AC: 35437 AN: 151980 Hom.: 8640 Cov.: 33

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.234 AC: 35543 AN: 152098 Hom.: 8686 Cov.: 33 AF XY: 0.234 AC XY: 17394 AN XY: 74356

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.0970

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0795

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.180

Alfa AF: 0.130 Hom.: 718

Bravo AF: 0.244

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3843776; hg19: chr20-23989652;