12-43105364-C-T

Variant names:

• chr12-43105364-C-T
• rs1167081

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 0.372 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.388 AC: 16082 AN: 41410

American (AMR) AF: 0.318 AC: 4856 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3468

East Asian (EAS) AF: 0.0843 AC: 435 AN: 5158

South Asian (SAS) AF: 0.423 AC: 2032 AN: 4806

European-Finnish (FIN) AF: 0.372 AC: 3930 AN: 10556

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26684 AN: 67958

Other (OTH) AF: 0.351 AC: 741 AN: 2110

Alfa AF: 0.388 Hom.: 1466

Bravo AF: 0.365

Asia WGS AF: 0.259 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.69
PhyloP100		0.049

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1167081;

hg19: chr12-43499167;