rs2425125

Variant names:

• chr20-35743032-G-A
• rs2425125
• ENST00000701255.2:n.622G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-35743032-G-A
• chr20-35743032-G-C
• chr20-35743032-G-T

Variant summary

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

The ENST00000701255.2(ENSG00000289872):​n.622G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 150,894 control chromosomes in the GnomAD database, including 5,738 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 0.26 (5738 hom., cov: 30)
• Consequence: ENSG00000289872 ENST00000701255.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 12 publications found

Genes affected

ENSG00000289872 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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
ENSG00000289872	ENST00000701255.2	n.622G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289872	ENST00000749779.1	n.495G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38547 AN: 150776 Hom.: 5688 Cov.: 30

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.256 AC: 38650 AN: 150894 Hom.: 5738 Cov.: 30 AF XY: 0.257 AC XY: 18883 AN XY: 73614

African (AFR) AF: 0.420 AC: 17227 AN: 40982

American (AMR) AF: 0.194 AC: 2944 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3468

East Asian (EAS) AF: 0.171 AC: 872 AN: 5112

South Asian (SAS) AF: 0.333 AC: 1589 AN: 4768

European-Finnish (FIN) AF: 0.186 AC: 1919 AN: 10322

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12546 AN: 67790

Other (OTH) AF: 0.253 AC: 530 AN: 2098

Alfa AF: 0.168 Hom.: 540

Bravo AF: 0.258

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.24
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2425125; hg19: chr20-34330954;