chr12-51942223-G-T

Variant names:

• chr12-51942223-G-T
• rs10783485

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 0.307 in 152,064 control chromosomes in the GnomAD database, including 9,356 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 0.31 (9356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.40
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.308 AC: 46728 AN: 151946 Hom.: 9350 Cov.: 32

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.307 AC: 46737 AN: 152064 Hom.: 9356 Cov.: 32 AF XY: 0.315 AC XY: 23406 AN XY: 74328

African (AFR) AF: 0.0880 AC: 3655 AN: 41546

American (AMR) AF: 0.503 AC: 7688 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3468

East Asian (EAS) AF: 0.762 AC: 3923 AN: 5150

South Asian (SAS) AF: 0.439 AC: 2113 AN: 4812

European-Finnish (FIN) AF: 0.329 AC: 3472 AN: 10566

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

European-Non Finnish (NFE) AF: 0.345 AC: 23454 AN: 67922

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.366 Hom.: 4048

Bravo AF: 0.318

Asia WGS AF: 0.533 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0060
DANN	Benign	0.57
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs10783485; hg19: chr12-52336007; COSMIC: COSV107181825;