rs7245046

chr18-54439198-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 0.167 in 152,090 control chromosomes in the GnomAD database, including 4,856 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 (4856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 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: 0.166 AC: 25260 AN: 151972 Hom.: 4831 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.167 AC: 25331 AN: 152090 Hom.: 4856 Cov.: 32 AF XY: 0.163 AC XY: 12133 AN XY: 74356

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.0800

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0467

Gnomad4 OTH AF: 0.124

Alfa AF: 0.122 Hom.: 391

Bravo AF: 0.182

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.29
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7245046; hg19: chr18-51965568;