chr12-108901732-T-C

Position:

• chr12-108901732-T-C

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 0.345 in 151,870 control chromosomes in the GnomAD database, including 9,680 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 0.35 (9680 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52357 AN: 151752 Hom.: 9661 Cov.: 30

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.345 AC: 52437 AN: 151870 Hom.: 9680 Cov.: 30 AF XY: 0.354 AC XY: 26268 AN XY: 74232

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.381

Alfa AF: 0.297 Hom.: 11224

Bravo AF: 0.366

Asia WGS AF: 0.414 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4964770; hg19: chr12-109295508;