rs2425895

Variant names:

• chr20-46707948-A-G
• rs2425895

Your query was ambiguous. Multiple possible variants found:

• chr20-46707948-A-G
• chr20-46707948-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.591 in 152,044 control chromosomes in the GnomAD database, including 27,618 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 0.59 (27618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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: 0.591 AC: 89779 AN: 151926 Hom.: 27571 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.591 AC: 89882 AN: 152044 Hom.: 27618 Cov.: 32 AF XY: 0.598 AC XY: 44485 AN XY: 74360

African (AFR) AF: 0.703 AC: 29155 AN: 41458

American (AMR) AF: 0.685 AC: 10466 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1837 AN: 3466

East Asian (EAS) AF: 0.925 AC: 4793 AN: 5182

South Asian (SAS) AF: 0.664 AC: 3203 AN: 4824

European-Finnish (FIN) AF: 0.529 AC: 5592 AN: 10564

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32936 AN: 67958

Other (OTH) AF: 0.589 AC: 1243 AN: 2110

Alfa AF: 0.536 Hom.: 42000

Bravo AF: 0.608

Asia WGS AF: 0.794 AC: 2758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.41
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2425895; hg19: chr20-45336587;