rs2425125

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701255.1(ENSG00000289872):​n.414G>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: ENST00000701255.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701255.1	n.414G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.253

Alfa AF: 0.161 Hom.: 477

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2425125; hg19: chr20-34330954;