12-43105364-C-T

Variant names:

• chr12-43105364-C-T
• rs1167081

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 0.372 in 151,920 control chromosomes in the GnomAD database, including 10,786 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 0.37 (10786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 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: 0.372 AC: 56489 AN: 151804 Hom.: 10775 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.372 AC: 56537 AN: 151920 Hom.: 10786 Cov.: 32 AF XY: 0.368 AC XY: 27315 AN XY: 74238

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.351

Alfa AF: 0.388 Hom.: 1407

Bravo AF: 0.365

Asia WGS AF: 0.259 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1167081; hg19: chr12-43499167;