chr12-100629801-T-C

Position:

• chr12-100629801-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 0.652 in 152,056 control chromosomes in the GnomAD database, including 32,914 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 0.65 (32914 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100629801T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99042 AN: 151938 Hom.: 32894 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.652 AC: 99102 AN: 152056 Hom.: 32914 Cov.: 32 AF XY: 0.655 AC XY: 48663 AN XY: 74332

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.667

Alfa AF: 0.665 Hom.: 5144

Bravo AF: 0.654

Asia WGS AF: 0.637 AC: 2214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10778056; hg19: chr12-101023579;