chr12-23524758-T-C

Variant names:

• chr12-23524758-T-C
• rs11046966

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 0.242 in 152,106 control chromosomes in the GnomAD database, including 5,149 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 0.24 (5149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.242 AC: 36824 AN: 151986 Hom.: 5149 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.242 AC: 36840 AN: 152106 Hom.: 5149 Cov.: 32 AF XY: 0.246 AC XY: 18299 AN XY: 74350

African (AFR) AF: 0.104 AC: 4330 AN: 41550

American (AMR) AF: 0.283 AC: 4328 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3464

East Asian (EAS) AF: 0.292 AC: 1509 AN: 5162

South Asian (SAS) AF: 0.188 AC: 909 AN: 4828

European-Finnish (FIN) AF: 0.392 AC: 4141 AN: 10574

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20167 AN: 67942

Other (OTH) AF: 0.253 AC: 534 AN: 2110

Alfa AF: 0.280 Hom.: 19024

Bravo AF: 0.237

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.0
DANN	Benign	0.80
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11046966; hg19: chr12-23677692;