rs41492957

Variant names:

• chr20-16988369-C-T
• rs41492957

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 0.131 in 152,004 control chromosomes in the GnomAD database, including 1,377 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 0.13 (1377 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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: 0.131 AC: 19894 AN: 151886 Hom.: 1375 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.131 AC: 19906 AN: 152004 Hom.: 1377 Cov.: 31 AF XY: 0.132 AC XY: 9777 AN XY: 74278

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.129

Alfa AF: 0.125 Hom.: 220

Bravo AF: 0.128

Asia WGS AF: 0.194 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41492957; hg19: chr20-16969014;