rs1504504

Variant names:

• chr18-51690266-T-C
• rs1504504

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 0.569 in 152,046 control chromosomes in the GnomAD database, including 26,591 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 0.57 (26591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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: 0.569 AC: 86468 AN: 151928 Hom.: 26564 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.569 AC: 86543 AN: 152046 Hom.: 26591 Cov.: 32 AF XY: 0.571 AC XY: 42467 AN XY: 74314

African (AFR) AF: 0.767 AC: 31823 AN: 41474

American (AMR) AF: 0.556 AC: 8497 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3470

East Asian (EAS) AF: 0.946 AC: 4891 AN: 5168

South Asian (SAS) AF: 0.547 AC: 2633 AN: 4816

European-Finnish (FIN) AF: 0.455 AC: 4805 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30500 AN: 67962

Other (OTH) AF: 0.544 AC: 1151 AN: 2114

Alfa AF: 0.507 Hom.: 2949

Bravo AF: 0.591

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.66
DANN	Benign	0.56
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1504504; hg19: chr18-49216636;