chr6-32889157-T-C

Variant names:

• chr6-32889157-T-C
• rs6936004

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 0.139 in 151,990 control chromosomes in the GnomAD database, including 1,715 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 (1715 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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: 0.138 AC: 21017 AN: 151876 Hom.: 1711 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.139 AC: 21057 AN: 151990 Hom.: 1715 Cov.: 32 AF XY: 0.139 AC XY: 10338 AN XY: 74306

African (AFR) AF: 0.222 AC: 9175 AN: 41396

American (AMR) AF: 0.100 AC: 1529 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3462

East Asian (EAS) AF: 0.0881 AC: 457 AN: 5186

South Asian (SAS) AF: 0.154 AC: 739 AN: 4814

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10594

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6943 AN: 67958

Other (OTH) AF: 0.128 AC: 269 AN: 2106

Alfa AF: 0.0536 Hom.: 52

Bravo AF: 0.138

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.91
DANN	Benign	0.36
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6936004; hg19: chr6-32856934;