12-43304529-T-C

Variant names:

• chr12-43304529-T-C
• rs10785424

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 0.523 in 152,122 control chromosomes in the GnomAD database, including 21,627 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 0.52 (21627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.523 AC: 79452 AN: 152004 Hom.: 21590 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.523 AC: 79552 AN: 152122 Hom.: 21627 Cov.: 32 AF XY: 0.528 AC XY: 39228 AN XY: 74352

African (AFR) AF: 0.576 AC: 23912 AN: 41494

American (AMR) AF: 0.598 AC: 9131 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1694 AN: 3464

East Asian (EAS) AF: 0.872 AC: 4517 AN: 5180

South Asian (SAS) AF: 0.646 AC: 3108 AN: 4810

European-Finnish (FIN) AF: 0.408 AC: 4315 AN: 10568

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31150 AN: 68010

Other (OTH) AF: 0.548 AC: 1155 AN: 2108

Alfa AF: 0.472 Hom.: 3575

Bravo AF: 0.541

Asia WGS AF: 0.760 AC: 2643 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	2.5
DANN	Benign	0.70
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs10785424; hg19: chr12-43698332;