12-27806972-C-T

Variant names:

• chr12-27806972-C-T
• rs7311374

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 0.098 in 151,814 control chromosomes in the GnomAD database, including 927 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 0.098 (927 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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: 0.0981 AC: 14880 AN: 151720 Hom.: 928 Cov.: 31

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0980 AC: 14874 AN: 151814 Hom.: 927 Cov.: 31 AF XY: 0.0957 AC XY: 7096 AN XY: 74146

African (AFR) AF: 0.0347 AC: 1437 AN: 41378

American (AMR) AF: 0.0921 AC: 1406 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3470

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5172

South Asian (SAS) AF: 0.126 AC: 606 AN: 4804

European-Finnish (FIN) AF: 0.0652 AC: 681 AN: 10452

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9856 AN: 67968

Other (OTH) AF: 0.0997 AC: 210 AN: 2106

Alfa AF: 0.116 Hom.: 936

Bravo AF: 0.0962

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs7311374; hg19: chr12-27959905;