rs1031825

chr20-4466836-A-Cchr20-4466836-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;