chr18-78473711-G-A

Variant names:

• chr18-78473711-G-A
• rs7233501

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 0.133 in 152,000 control chromosomes in the GnomAD database, including 1,727 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 0.13 (1727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20235 AN: 151882 Hom.: 1727 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.00731

Gnomad SAS AF: 0.0955

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.133 AC: 20257 AN: 152000 Hom.: 1727 Cov.: 33 AF XY: 0.132 AC XY: 9836 AN XY: 74328

African (AFR) AF: 0.217 AC: 8947 AN: 41290

American (AMR) AF: 0.0789 AC: 1208 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 298 AN: 3472

East Asian (EAS) AF: 0.00733 AC: 38 AN: 5184

South Asian (SAS) AF: 0.0958 AC: 462 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10594

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7519 AN: 68012

Other (OTH) AF: 0.107 AC: 227 AN: 2114

Alfa AF: 0.118 Hom.: 2093

Bravo AF: 0.133

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.43
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs7233501; hg19: chr18-76233711;