6-29008294-T-C

Position:

• chr6-29008294-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 0.343 in 152,074 control chromosomes in the GnomAD database, including 10,413 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 0.34 (10413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 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: 0.343 AC: 52172 AN: 151956 Hom.: 10392 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.343 AC: 52233 AN: 152074 Hom.: 10413 Cov.: 32 AF XY: 0.346 AC XY: 25688 AN XY: 74324

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.338

Alfa AF: 0.274 Hom.: 3969

Bravo AF: 0.356

Asia WGS AF: 0.278 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6923005; hg19: chr6-28976071;