rs2734925

Variant names:

• chr6-29913570-G-C
• rs2734925

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 0.685 in 144,372 control chromosomes in the GnomAD database, including 35,994 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 0.68 (35994 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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: 0.685 AC: 98801 AN: 144272 Hom.: 35987 Cov.: 29

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.685 AC: 98841 AN: 144372 Hom.: 35994 Cov.: 29 AF XY: 0.682 AC XY: 48004 AN XY: 70370

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.663

Alfa AF: 0.696 Hom.: 4217

Asia WGS AF: 0.685 AC: 2138 AN: 3118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734925; hg19: chr6-29881347;