12-125850918-T-C

Variant names:

• chr12-125850918-T-C
• rs2108521

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 0.296 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.335

Alfa AF: 0.273 Hom.: 3107

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2108521; hg19: chr12-126335464;