18-51731975-G-A

Variant names:

• chr18-51731975-G-A
• rs748317

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 0.594 in 152,082 control chromosomes in the GnomAD database, including 29,251 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 0.59 (29251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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: 0.593 AC: 90187 AN: 151964 Hom.: 29211 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.594 AC: 90277 AN: 152082 Hom.: 29251 Cov.: 32 AF XY: 0.596 AC XY: 44298 AN XY: 74350

African (AFR) AF: 0.834 AC: 34623 AN: 41502

American (AMR) AF: 0.565 AC: 8635 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1709 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4848 AN: 5174

South Asian (SAS) AF: 0.547 AC: 2636 AN: 4818

European-Finnish (FIN) AF: 0.468 AC: 4951 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31075 AN: 67952

Other (OTH) AF: 0.563 AC: 1188 AN: 2110

Alfa AF: 0.521 Hom.: 35360

Bravo AF: 0.617

Asia WGS AF: 0.749 AC: 2606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.56
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs748317; hg19: chr18-49258345;