rs2743941

chr6-29787674-T-Cchr6-29787674-T-G

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 0.741 in 152,032 control chromosomes in the GnomAD database, including 41,888 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 0.74 (41888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.807 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: 0.741 AC: 112559 AN: 151912 Hom.: 41829 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.741 AC: 112675 AN: 152032 Hom.: 41888 Cov.: 32 AF XY: 0.737 AC XY: 54749 AN XY: 74302

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.750

Alfa AF: 0.760 Hom.: 56799

Bravo AF: 0.754

Asia WGS AF: 0.716 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.38
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2743941; hg19: chr6-29755451;