12-58401580-G-T

Variant names:

• chr12-58401580-G-T
• rs3916105

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 0.101 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.100 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

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0441

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0425

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.0757

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3916105; hg19: chr12-58795363;