6-29913048-T-C

Position:

• chr6-29913048-T-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 0.827 in 145,924 control chromosomes in the GnomAD database, including 52,269 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 0.83 (52269 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.827 AC: 120551 AN: 145814 Hom.: 52216 Cov.: 28

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.827 AC: 120660 AN: 145924 Hom.: 52269 Cov.: 28 AF XY: 0.823 AC XY: 58422 AN XY: 71020

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.847

Alfa AF: 0.812 Hom.: 5376

Asia WGS AF: 0.928 AC: 2888 AN: 3112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611442; hg19: chr6-29880825;