6-32702478-C-T

Variant names:

• chr6-32702478-C-T
• rs2856718

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 0.35 in 151,944 control chromosomes in the GnomAD database, including 9,717 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 (9717 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 127 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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: 0.350 AC: 53143 AN: 151824 Hom.: 9719 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.350 AC: 53157 AN: 151944 Hom.: 9717 Cov.: 31 AF XY: 0.344 AC XY: 25579 AN XY: 74278

African (AFR) AF: 0.340 AC: 14071 AN: 41400

American (AMR) AF: 0.343 AC: 5231 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1555 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2696 AN: 5178

South Asian (SAS) AF: 0.468 AC: 2252 AN: 4810

European-Finnish (FIN) AF: 0.189 AC: 1992 AN: 10552

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24033 AN: 67952

Other (OTH) AF: 0.401 AC: 844 AN: 2106

Alfa AF: 0.358 Hom.: 29829

Bravo AF: 0.360

Asia WGS AF: 0.493 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.5
DANN	Benign	0.76
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2856718; hg19: chr6-32670255;