chr6-32884870-T-C

Variant names:

• chr6-32884870-T-C
• rs2187689

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 0.14 in 151,730 control chromosomes in the GnomAD database, including 1,807 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 0.14 (1807 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21103 AN: 151614 Hom.: 1795 Cov.: 30

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.140 AC: 21167 AN: 151730 Hom.: 1807 Cov.: 30 AF XY: 0.141 AC XY: 10490 AN XY: 74160

African (AFR) AF: 0.220 AC: 9084 AN: 41334

American (AMR) AF: 0.156 AC: 2373 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3462

East Asian (EAS) AF: 0.178 AC: 923 AN: 5180

South Asian (SAS) AF: 0.195 AC: 939 AN: 4804

European-Finnish (FIN) AF: 0.0790 AC: 829 AN: 10488

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0887 AC: 6023 AN: 67914

Other (OTH) AF: 0.140 AC: 294 AN: 2100

Alfa AF: 0.107 Hom.: 1814

Bravo AF: 0.146

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2187689; hg19: chr6-32852647;