12-107124858-C-T

Variant names:

• chr12-107124858-C-T
• rs4964521

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 0.417 in 151,686 control chromosomes in the GnomAD database, including 13,325 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 0.42 (13325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63113 AN: 151568 Hom.: 13292 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.417 AC: 63204 AN: 151686 Hom.: 13325 Cov.: 31 AF XY: 0.416 AC XY: 30859 AN XY: 74138

African (AFR) AF: 0.445 AC: 18391 AN: 41328

American (AMR) AF: 0.480 AC: 7309 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3466

East Asian (EAS) AF: 0.459 AC: 2373 AN: 5166

South Asian (SAS) AF: 0.398 AC: 1905 AN: 4792

European-Finnish (FIN) AF: 0.361 AC: 3781 AN: 10478

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26806 AN: 67922

Other (OTH) AF: 0.398 AC: 836 AN: 2102

Alfa AF: 0.405 Hom.: 52793

Bravo AF: 0.428

Asia WGS AF: 0.388 AC: 1347 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4964521; hg19: chr12-107518636;