rs7233501

Positions:

• chr18-78473711-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;