rs4141461

Variant names:

• chr20-25101525-G-A
• rs4141461

Your query was ambiguous. Multiple possible variants found:

• chr20-25101525-G-A
• chr20-25101525-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;