18-51787215-T-C

Variant names:

• chr18-51787215-T-C
• rs1504508

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 0.413 in 152,054 control chromosomes in the GnomAD database, including 17,396 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 0.41 (17396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.768 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: 0.413 AC: 62698 AN: 151938 Hom.: 17362 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.413 AC: 62779 AN: 152054 Hom.: 17396 Cov.: 32 AF XY: 0.415 AC XY: 30834 AN XY: 74346

African (AFR) AF: 0.775 AC: 32165 AN: 41494

American (AMR) AF: 0.361 AC: 5514 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3468

East Asian (EAS) AF: 0.675 AC: 3488 AN: 5164

South Asian (SAS) AF: 0.370 AC: 1785 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2398 AN: 10568

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15085 AN: 67954

Other (OTH) AF: 0.387 AC: 818 AN: 2114

Alfa AF: 0.286 Hom.: 2217

Bravo AF: 0.444

Asia WGS AF: 0.547 AC: 1904 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	0.021
DANN	Benign	0.35
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1504508; hg19: chr18-49313585;