6-134166530-T-C

Variant names:

• chr6-134166530-T-C
• rs2758151

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.411 AC: 17039 AN: 41444

American (AMR) AF: 0.272 AC: 4166 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2861 AN: 5154

South Asian (SAS) AF: 0.316 AC: 1519 AN: 4800

European-Finnish (FIN) AF: 0.421 AC: 4447 AN: 10560

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21652 AN: 67978

Other (OTH) AF: 0.324 AC: 686 AN: 2116

Alfa AF: 0.321 Hom.: 11148

Bravo AF: 0.345

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.24
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2758151; hg19: chr6-134487668;