rs1788776

Variant names:

• chr18-23664073-G-A
• rs1788776

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 0.637 in 152,100 control chromosomes in the GnomAD database, including 31,068 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 0.64 (31068 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.697 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: 0.636 AC: 96734 AN: 151980 Hom.: 31030 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.637 AC: 96833 AN: 152100 Hom.: 31068 Cov.: 33 AF XY: 0.636 AC XY: 47255 AN XY: 74334

African (AFR) AF: 0.647 AC: 26845 AN: 41478

American (AMR) AF: 0.708 AC: 10822 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2439 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2203 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2868 AN: 4826

European-Finnish (FIN) AF: 0.613 AC: 6474 AN: 10564

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42858 AN: 67992

Other (OTH) AF: 0.643 AC: 1356 AN: 2108

Alfa AF: 0.635 Hom.: 48702

Bravo AF: 0.646

Asia WGS AF: 0.518 AC: 1802 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.59
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs1788776; hg19: chr18-21244037;