chr18-48460768-T-A

Position:

• chr18-48460768-T-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 0.826 in 152,112 control chromosomes in the GnomAD database, including 53,355 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 0.83 (53355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

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 (NFE) allele frequency at 95% confidence interval = 0.933 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: 0.826 AC: 125580 AN: 151994 Hom.: 53330 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.826 AC: 125650 AN: 152112 Hom.: 53355 Cov.: 31 AF XY: 0.824 AC XY: 61232 AN XY: 74344

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.939

Gnomad4 OTH AF: 0.850

Alfa AF: 0.875 Hom.: 7368

Bravo AF: 0.809

Asia WGS AF: 0.843 AC: 2932 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	0.43
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1398193; hg19: chr18-45987139;