6-31842308-G-T

Variant names:

• chr6-31842308-G-T
• rs3115673

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 0.224 in 152,022 control chromosomes in the GnomAD database, including 4,409 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 0.22 (4409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.224 AC: 34014 AN: 151904 Hom.: 4405 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.224 AC: 34053 AN: 152022 Hom.: 4409 Cov.: 32 AF XY: 0.232 AC XY: 17255 AN XY: 74328

African (AFR) AF: 0.322 AC: 13334 AN: 41418

American (AMR) AF: 0.261 AC: 3981 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1043 AN: 5170

South Asian (SAS) AF: 0.244 AC: 1179 AN: 4826

European-Finnish (FIN) AF: 0.333 AC: 3518 AN: 10580

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10190 AN: 67982

Other (OTH) AF: 0.204 AC: 429 AN: 2108

Alfa AF: 0.168 Hom.: 9792

Bravo AF: 0.222

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs3115673; hg19: chr6-31810085;