chr6-29681279-C-T

Position:

• chr6-29681279-C-T

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 0.351 in 151,254 control chromosomes in the GnomAD database, including 9,823 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 0.35 (9823 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 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: 0.351 AC: 53026 AN: 151138 Hom.: 9812 Cov.: 27

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.351 AC: 53074 AN: 151254 Hom.: 9823 Cov.: 27 AF XY: 0.349 AC XY: 25773 AN XY: 73852

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.391

Alfa AF: 0.347 Hom.: 10496

Bravo AF: 0.374

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129054; hg19: chr6-29649056;