6-29817458-C-T

Variant names:

• chr6-29817458-C-T
• rs1619379

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;