12-114905687-C-T

Variant names:

• chr12-114905687-C-T
• rs7963771

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 0.334 in 151,942 control chromosomes in the GnomAD database, including 8,813 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 0.33 (8813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.404 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: 0.334 AC: 50755 AN: 151822 Hom.: 8797 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.334 AC: 50813 AN: 151942 Hom.: 8813 Cov.: 32 AF XY: 0.332 AC XY: 24622 AN XY: 74262

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.369

Alfa AF: 0.321 Hom.: 3747

Bravo AF: 0.349

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7963771; hg19: chr12-115343492;