12-51926293-C-T

Variant names:

• chr12-51926293-C-T
• rs1979921

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.0423 in 152,294 control chromosomes in the GnomAD database, including 155 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 0.042 (155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0423 (6444/152294) while in subpopulation NFE AF = 0.0459 (3121/68014). AF 95% confidence interval is 0.0445. There are 155 homozygotes in GnomAd4. There are 3141 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 155 gene

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: 0.0423 AC: 6431 AN: 152176 Hom.: 151 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0423 AC: 6444 AN: 152294 Hom.: 155 Cov.: 32 AF XY: 0.0422 AC XY: 3141 AN XY: 74474

African (AFR) AF: 0.0444 AC: 1845 AN: 41556

American (AMR) AF: 0.0343 AC: 525 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0331 AC: 160 AN: 4830

European-Finnish (FIN) AF: 0.0368 AC: 391 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0459 AC: 3121 AN: 68014

Other (OTH) AF: 0.0445 AC: 94 AN: 2114

Alfa AF: 0.0398 Hom.: 88

Bravo AF: 0.0423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs1979921; hg19: chr12-52320077;