12-100629801-T-C

Variant names:

• chr12-100629801-T-C
• rs10778056

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 0.652 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.518 AC: 21476 AN: 41436

American (AMR) AF: 0.752 AC: 11488 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3472

East Asian (EAS) AF: 0.783 AC: 4055 AN: 5178

South Asian (SAS) AF: 0.545 AC: 2628 AN: 4818

European-Finnish (FIN) AF: 0.723 AC: 7650 AN: 10574

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47218 AN: 67978

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10778056; hg19: chr12-101023579;