rs2734925

chr6-29913570-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;