rs7294919

Positions:

• chr12-116889787-T-C
• chr12-116889787-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.183 in 152,062 control chromosomes in the GnomAD database, including 3,701 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 0.18 (3701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27792 AN: 151944 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.183 AC: 27835 AN: 152062 Hom.: 3701 Cov.: 32 AF XY: 0.179 AC XY: 13323 AN XY: 74348

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0854

Gnomad4 FIN AF: 0.0764

Gnomad4 NFE AF: 0.0978

Gnomad4 OTH AF: 0.188

Alfa AF: 0.113 Hom.: 2297

Bravo AF: 0.198

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7294919; hg19: chr12-117327592;