6-31240143-C-T

Variant names:

• chr6-31240143-C-T
• rs3132499

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 0.882 in 152,002 control chromosomes in the GnomAD database, including 59,199 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 0.88 (59199 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.882 AC: 133894 AN: 151886 Hom.: 59144 Cov.: 30

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.882 AC: 134004 AN: 152002 Hom.: 59199 Cov.: 30 AF XY: 0.882 AC XY: 65489 AN XY: 74266

African (AFR) AF: 0.934 AC: 38720 AN: 41458

American (AMR) AF: 0.876 AC: 13377 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3376 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4331 AN: 5160

South Asian (SAS) AF: 0.872 AC: 4208 AN: 4824

European-Finnish (FIN) AF: 0.852 AC: 8946 AN: 10506

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58072 AN: 67998

Other (OTH) AF: 0.908 AC: 1916 AN: 2110

Alfa AF: 0.869 Hom.: 178491

Bravo AF: 0.887

Asia WGS AF: 0.876 AC: 3049 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	0.91
DANN	Benign	0.40
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs3132499; hg19: chr6-31207920;