12-10331415-C-T

Variant names:

• chr12-10331415-C-T
• rs12310310

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 0.271 in 152,090 control chromosomes in the GnomAD database, including 6,431 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 0.27 (6431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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: 0.271 AC: 41120 AN: 151972 Hom.: 6413 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.271 AC: 41177 AN: 152090 Hom.: 6431 Cov.: 32 AF XY: 0.264 AC XY: 19651 AN XY: 74344

African (AFR) AF: 0.434 AC: 17995 AN: 41490

American (AMR) AF: 0.179 AC: 2737 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3470

East Asian (EAS) AF: 0.113 AC: 584 AN: 5176

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2066 AN: 10576

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.223 AC: 15155 AN: 67984

Other (OTH) AF: 0.252 AC: 533 AN: 2116

Alfa AF: 0.233 Hom.: 18825

Bravo AF: 0.276

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.29
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs12310310; hg19: chr12-10484014;