rs2731006

Variant names:

• chr12-42767023-C-T
• rs2731006

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 0.146 in 151,664 control chromosomes in the GnomAD database, including 2,140 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 0.15 (2140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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: 0.146 AC: 22195 AN: 151546 Hom.: 2134 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.146 AC: 22206 AN: 151664 Hom.: 2140 Cov.: 32 AF XY: 0.153 AC XY: 11364 AN XY: 74114

African (AFR) AF: 0.0349 AC: 1442 AN: 41318

American (AMR) AF: 0.129 AC: 1970 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1744 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1359 AN: 4794

European-Finnish (FIN) AF: 0.265 AC: 2789 AN: 10510

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 11996 AN: 67886

Other (OTH) AF: 0.155 AC: 324 AN: 2094

Alfa AF: 0.156 Hom.: 378

Bravo AF: 0.128

Asia WGS AF: 0.331 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2731006; hg19: chr12-43160825;