6-29817458-C-T

Position:

• chr6-29817458-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 0.398 in 152,028 control chromosomes in the GnomAD database, including 12,125 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 0.40 (12125 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29817458C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60378 AN: 151910 Hom.: 12107 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.398 AC: 60441 AN: 152028 Hom.: 12125 Cov.: 32 AF XY: 0.393 AC XY: 29182 AN XY: 74308

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.418

Alfa AF: 0.415 Hom.: 20454

Bravo AF: 0.408

Asia WGS AF: 0.382 AC: 1331 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	0.22
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1619379; hg19: chr6-29785235;