12-120125170-C-T

Variant names:

• chr12-120125170-C-T
• rs11065028

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 0.628 in 152,046 control chromosomes in the GnomAD database, including 30,128 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 0.63 (30128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.628 AC: 95446 AN: 151928 Hom.: 30091 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.628 AC: 95540 AN: 152046 Hom.: 30128 Cov.: 32 AF XY: 0.628 AC XY: 46682 AN XY: 74300

African (AFR) AF: 0.688 AC: 28531 AN: 41460

American (AMR) AF: 0.664 AC: 10139 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1763 AN: 3472

East Asian (EAS) AF: 0.539 AC: 2794 AN: 5182

South Asian (SAS) AF: 0.670 AC: 3233 AN: 4824

European-Finnish (FIN) AF: 0.611 AC: 6460 AN: 10568

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40579 AN: 67952

Other (OTH) AF: 0.624 AC: 1320 AN: 2114

Alfa AF: 0.610 Hom.: 51358

Bravo AF: 0.632

Asia WGS AF: 0.651 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.76
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs11065028; hg19: chr12-120562974;