rs7239408

chr18-53906430-G-Achr18-53906430-G-T

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 0.271 in 151,864 control chromosomes in the GnomAD database, including 6,070 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 0.27 (6070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.271 AC: 41147 AN: 151746 Hom.: 6060 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0489

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.271 AC: 41180 AN: 151864 Hom.: 6070 Cov.: 32 AF XY: 0.268 AC XY: 19870 AN XY: 74172

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0490

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.260

Alfa AF: 0.243 Hom.: 7719

Bravo AF: 0.271

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.11
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7239408; hg19: chr18-51432800;