18-51908404-G-A

Position:

• chr18-51908404-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 0.0918 in 152,170 control chromosomes in the GnomAD database, including 865 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 0.092 (865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13963 AN: 152052 Hom.: 866 Cov.: 32

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.0898

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0918 AC: 13965 AN: 152170 Hom.: 865 Cov.: 32 AF XY: 0.0892 AC XY: 6639 AN XY: 74388

Gnomad4 AFR AF: 0.0237

Gnomad4 AMR AF: 0.0919

Gnomad4 ASJ AF: 0.0898

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.112

Alfa AF: 0.130 Hom.: 1836

Bravo AF: 0.0861

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520815; hg19: chr18-49434774;