chr6-29787674-T-C

Variant names:

• chr6-29787674-T-C
• rs2743941

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;