12-126496109-C-T

Variant names:

• chr12-126496109-C-T
• rs10847171

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 0.585 in 152,064 control chromosomes in the GnomAD database, including 30,186 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 0.59 (30186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.586 AC: 89002 AN: 151946 Hom.: 30176 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.585 AC: 89025 AN: 152064 Hom.: 30186 Cov.: 32 AF XY: 0.590 AC XY: 43859 AN XY: 74312

African (AFR) AF: 0.217 AC: 8983 AN: 41468

American (AMR) AF: 0.730 AC: 11155 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2067 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4653 AN: 5166

South Asian (SAS) AF: 0.672 AC: 3238 AN: 4818

European-Finnish (FIN) AF: 0.720 AC: 7597 AN: 10554

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49238 AN: 67994

Other (OTH) AF: 0.611 AC: 1290 AN: 2112

Alfa AF: 0.668 Hom.: 42259

Bravo AF: 0.575

Asia WGS AF: 0.774 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10847171; hg19: chr12-126980655;