12-125850918-T-C

Variant names:

• chr12-125850918-T-C
• rs2108521

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 0.296 in 152,186 control chromosomes in the GnomAD database, including 6,998 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 0.30 (6998 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 3 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 = 0.481 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: 0.296 AC: 44976 AN: 152068 Hom.: 6994 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.296 AC: 45006 AN: 152186 Hom.: 6998 Cov.: 33 AF XY: 0.303 AC XY: 22526 AN XY: 74402

African (AFR) AF: 0.281 AC: 11671 AN: 41510

American (AMR) AF: 0.406 AC: 6218 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1004 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2565 AN: 5162

South Asian (SAS) AF: 0.368 AC: 1777 AN: 4826

European-Finnish (FIN) AF: 0.303 AC: 3214 AN: 10608

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17501 AN: 67996

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.272 Hom.: 3378

Bravo AF: 0.307

Asia WGS AF: 0.371 AC: 1290 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	5.9
DANN	Benign	0.81
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2108521; hg19: chr12-126335464;