rs2425895

Positions:

• chr20-46707948-A-G
• chr20-46707948-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 0.591 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.46707948A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.589

Alfa AF: 0.520 Hom.: 6119

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2425895; hg19: chr20-45336587;