rs7245046

Variant names:

• chr18-54439198-G-A
• rs7245046

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 0.167 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.473 AC: 19601 AN: 41412

American (AMR) AF: 0.0800 AC: 1221 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5176

South Asian (SAS) AF: 0.0958 AC: 462 AN: 4822

European-Finnish (FIN) AF: 0.0313 AC: 332 AN: 10610

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3176 AN: 68018

Other (OTH) AF: 0.124 AC: 262 AN: 2112

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
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs7245046; hg19: chr18-51965568;