rs7233501

Variant names:

• chr18-78473711-G-A
• rs7233501

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.133 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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.0789

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.00733

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.107

Alfa AF: 0.116 Hom.: 493

Bravo AF: 0.133

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7233501; hg19: chr18-76233711;