12-58401580-G-T

Variant names:

• chr12-58401580-G-T
• rs3916105

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 0.101 in 151,904 control chromosomes in the GnomAD database, including 1,823 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 0.10 (1823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15245 AN: 151786 Hom.: 1809 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.101 AC: 15303 AN: 151904 Hom.: 1823 Cov.: 32 AF XY: 0.0988 AC XY: 7333 AN XY: 74256

African (AFR) AF: 0.287 AC: 11856 AN: 41374

American (AMR) AF: 0.0441 AC: 671 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3466

East Asian (EAS) AF: 0.118 AC: 609 AN: 5162

South Asian (SAS) AF: 0.0425 AC: 205 AN: 4824

European-Finnish (FIN) AF: 0.0293 AC: 310 AN: 10584

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1307 AN: 67942

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

Alfa AF: 0.00487 Hom.: 4

Bravo AF: 0.110

Asia WGS AF: 0.124 AC: 430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.34
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs3916105; hg19: chr12-58795363;