rs12524744

Variant names:

• chr6-18114889-C-T
• rs12524744

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 0.0513 in 152,160 control chromosomes in the GnomAD database, including 284 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 0.051 (284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 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: 0.0513 AC: 7797 AN: 152042 Hom.: 281 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0513 AC: 7805 AN: 152160 Hom.: 284 Cov.: 32 AF XY: 0.0524 AC XY: 3900 AN XY: 74378

African (AFR) AF: 0.0150 AC: 624 AN: 41516

American (AMR) AF: 0.113 AC: 1724 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3466

East Asian (EAS) AF: 0.165 AC: 851 AN: 5170

South Asian (SAS) AF: 0.0508 AC: 245 AN: 4824

European-Finnish (FIN) AF: 0.0452 AC: 479 AN: 10588

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0520 AC: 3538 AN: 68010

Other (OTH) AF: 0.0541 AC: 114 AN: 2108

Alfa AF: 0.0549 Hom.: 557

Bravo AF: 0.0556

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.45
PhyloP100		-1.5

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: rs12524744;

hg19: chr6-18115120;