18-50760187-G-A

Variant names:

• chr18-50760187-G-A
• rs17735726

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 0.0779 in 151,542 control chromosomes in the GnomAD database, including 676 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 0.078 (676 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11803 AN: 151442 Hom.: 675 Cov.: 30

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.000973

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0791

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

GnomAD4 genome AF: 0.0779 AC: 11805 AN: 151542 Hom.: 676 Cov.: 30 AF XY: 0.0773 AC XY: 5715 AN XY: 73970

African (AFR) AF: 0.0203 AC: 839 AN: 41332

American (AMR) AF: 0.151 AC: 2291 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3468

East Asian (EAS) AF: 0.000975 AC: 5 AN: 5126

South Asian (SAS) AF: 0.0237 AC: 113 AN: 4776

European-Finnish (FIN) AF: 0.0979 AC: 1020 AN: 10414

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.104 AC: 7074 AN: 67922

Other (OTH) AF: 0.0783 AC: 164 AN: 2094

Alfa AF: 0.0864 Hom.: 408

Bravo AF: 0.0809

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs17735726; hg19: chr18-48286557;