12-132614597-G-T

Variant names:

• chr12-132614597-G-T
• rs11614717

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 0.152 in 151,602 control chromosomes in the GnomAD database, including 1,897 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 (1897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23080 AN: 151482 Hom.: 1888 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.152 AC: 23109 AN: 151602 Hom.: 1897 Cov.: 32 AF XY: 0.153 AC XY: 11307 AN XY: 74092

African (AFR) AF: 0.130 AC: 5380 AN: 41404

American (AMR) AF: 0.194 AC: 2953 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3468

East Asian (EAS) AF: 0.162 AC: 839 AN: 5174

South Asian (SAS) AF: 0.0692 AC: 333 AN: 4814

European-Finnish (FIN) AF: 0.146 AC: 1539 AN: 10542

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10965 AN: 67632

Other (OTH) AF: 0.133 AC: 282 AN: 2114

Alfa AF: 0.154 Hom.: 935

Bravo AF: 0.156

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.39
DANN	Benign	0.14
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11614717; hg19: chr12-133191183;