6-29768270-T-C

Position:

• chr6-29768270-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 0.731 in 151,954 control chromosomes in the GnomAD database, including 41,327 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 0.73 (41327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 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: 0.731 AC: 111006 AN: 151838 Hom.: 41283 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.731 AC: 111093 AN: 151954 Hom.: 41327 Cov.: 33 AF XY: 0.721 AC XY: 53558 AN XY: 74300

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.727

Alfa AF: 0.712 Hom.: 57099

Bravo AF: 0.753

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1737043; hg19: chr6-29736047;