rs6725189

Variant names:

• chr2-20996129-G-T
• rs6725189

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 0.184 in 152,142 control chromosomes in the GnomAD database, including 2,718 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 0.18 (2718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 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: 0.184 AC: 27944 AN: 152024 Hom.: 2711 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.184 AC: 27978 AN: 152142 Hom.: 2718 Cov.: 32 AF XY: 0.184 AC XY: 13708 AN XY: 74386

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0735

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.207

Alfa AF: 0.203 Hom.: 4466

Bravo AF: 0.185

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6725189; hg19: chr2-21219001;