12-107156643-G-T

Variant names:

• chr12-107156643-G-T
• rs7306232

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 0.311 in 152,048 control chromosomes in the GnomAD database, including 8,960 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 0.31 (8960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.41 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: 0.311 AC: 47310 AN: 151930 Hom.: 8950 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.311 AC: 47344 AN: 152048 Hom.: 8960 Cov.: 32 AF XY: 0.314 AC XY: 23341 AN XY: 74298

Gnomad4 AFR AF: 0.0940

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.347

Alfa AF: 0.358 Hom.: 6268

Bravo AF: 0.307

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7306232; hg19: chr12-107550421;