chr6-31230932-C-T

Variant names:

• chr6-31230932-C-T
• rs6908994

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 0.167 in 152,070 control chromosomes in the GnomAD database, including 2,255 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 0.17 (2255 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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: 0.167 AC: 25396 AN: 151952 Hom.: 2253 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.167 AC: 25406 AN: 152070 Hom.: 2255 Cov.: 33 AF XY: 0.167 AC XY: 12431 AN XY: 74316

African (AFR) AF: 0.166 AC: 6898 AN: 41478

American (AMR) AF: 0.197 AC: 3005 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3466

East Asian (EAS) AF: 0.220 AC: 1139 AN: 5184

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4824

European-Finnish (FIN) AF: 0.211 AC: 2222 AN: 10542

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11463 AN: 67972

Other (OTH) AF: 0.133 AC: 280 AN: 2108

Alfa AF: 0.171 Hom.: 7613

Bravo AF: 0.168

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.66
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6908994; hg19: chr6-31198709;