rs7294372

Variant names:

• chr12-114199618-T-C
• rs7294372

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 0.0397 in 152,092 control chromosomes in the GnomAD database, including 163 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 0.040 (163 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0747 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6041 AN: 151972 Hom.: 162 Cov.: 33

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.0455

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0397 AC: 6040 AN: 152092 Hom.: 163 Cov.: 33 AF XY: 0.0404 AC XY: 3003 AN XY: 74346

African (AFR) AF: 0.0547 AC: 2273 AN: 41522

American (AMR) AF: 0.0461 AC: 703 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3462

East Asian (EAS) AF: 0.0811 AC: 420 AN: 5176

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4822

European-Finnish (FIN) AF: 0.0455 AC: 481 AN: 10572

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0241 AC: 1639 AN: 67976

Other (OTH) AF: 0.0413 AC: 87 AN: 2106

Alfa AF: 0.0297 Hom.: 428

Bravo AF: 0.0419

Asia WGS AF: 0.0550 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.76
DANN	Benign	0.29
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7294372; hg19: chr12-114637423;