rs7242459

Variant names:

• chr18-51153619-C-A
• rs7242459

Your query was ambiguous. Multiple possible variants found:

• chr18-51153619-C-A
• chr18-51153619-C-G

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 0.345 in 152,078 control chromosomes in the GnomAD database, including 10,085 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 0.35 (10085 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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: 0.345 AC: 52476 AN: 151960 Hom.: 10092 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.345 AC: 52475 AN: 152078 Hom.: 10085 Cov.: 33 AF XY: 0.343 AC XY: 25480 AN XY: 74342

African (AFR) AF: 0.188 AC: 7806 AN: 41504

American (AMR) AF: 0.344 AC: 5264 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1507 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1225 AN: 5174

South Asian (SAS) AF: 0.349 AC: 1683 AN: 4820

European-Finnish (FIN) AF: 0.405 AC: 4277 AN: 10564

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29555 AN: 67948

Other (OTH) AF: 0.353 AC: 745 AN: 2108

Alfa AF: 0.268 Hom.: 788

Bravo AF: 0.330

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.7
DANN	Benign	0.90
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs7242459; hg19: chr18-48679989;