chr12-107156643-G-T

Variant names:

• chr12-107156643-G-T
• rs7306232

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 0.311 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0940 AC: 3900 AN: 41488

American (AMR) AF: 0.419 AC: 6396 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2056 AN: 5156

South Asian (SAS) AF: 0.292 AC: 1408 AN: 4818

European-Finnish (FIN) AF: 0.360 AC: 3803 AN: 10556

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27478 AN: 67972

Other (OTH) AF: 0.347 AC: 732 AN: 2108

Alfa AF: 0.369 Hom.: 9165

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7306232; hg19: chr12-107550421;