rs1031825

Variant names:

• chr20-4466836-A-C
• rs1031825

Your query was ambiguous. Multiple possible variants found:

• chr20-4466836-A-C
• chr20-4466836-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 0.625 in 151,228 control chromosomes in the GnomAD database, including 30,739 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 0.63 (30739 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.625 AC: 94493 AN: 151110 Hom.: 30721 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.625 AC: 94560 AN: 151228 Hom.: 30739 Cov.: 31 AF XY: 0.627 AC XY: 46332 AN XY: 73924

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.636

Alfa AF: 0.615 Hom.: 3045

Bravo AF: 0.619

Asia WGS AF: 0.561 AC: 1951 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
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: rs1031825; hg19: chr20-4447483;