rs7233060

Variant names:

• chr18-79632379-G-A
• rs7233060

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 0.173 in 152,164 control chromosomes in the GnomAD database, including 2,426 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 0.17 (2426 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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: 0.173 AC: 26259 AN: 152048 Hom.: 2415 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0545

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.173 AC: 26295 AN: 152164 Hom.: 2426 Cov.: 33 AF XY: 0.170 AC XY: 12615 AN XY: 74396

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.173

Alfa AF: 0.169 Hom.: 2390

Bravo AF: 0.174

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7233060; hg19: chr18-77392379;