6-134166530-T-C

Variant names:

• chr6-134166530-T-C
• rs2758151

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 0.354 in 152,020 control chromosomes in the GnomAD database, including 9,928 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 (9928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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: 0.354 AC: 53759 AN: 151902 Hom.: 9920 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.354 AC: 53812 AN: 152020 Hom.: 9928 Cov.: 32 AF XY: 0.361 AC XY: 26790 AN XY: 74296

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.324

Alfa AF: 0.319 Hom.: 7196

Bravo AF: 0.345

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2758151; hg19: chr6-134487668;