rs4141461

chr20-25101525-G-Achr20-25101525-G-C

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 0.829 in 152,178 control chromosomes in the GnomAD database, including 52,491 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 0.83 (52491 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.829 AC: 126096 AN: 152060 Hom.: 52455 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.829 AC: 126186 AN: 152178 Hom.: 52491 Cov.: 32 AF XY: 0.835 AC XY: 62134 AN XY: 74398

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.852

Alfa AF: 0.816 Hom.: 62316

Bravo AF: 0.832

Asia WGS AF: 0.950 AC: 3302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4141461; hg19: chr20-25082161;