18-48460768-T-A

Variant names:

• chr18-48460768-T-A
• rs1398193
• ENST00000751899.1:n.338+21298A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751899.1(ENSG00000297938):​n.338+21298A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000297938 ENST00000751899.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 2 publications found

Genes affected

ENSG00000297938 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751899.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297938	ENST00000751899.1		n.338+21298A>T		intron	N/A
	ENSG00000297938	ENST00000751900.1		n.281+22323A>T		intron	N/A

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

African (AFR) AF: 0.617 AC: 25587 AN: 41450

American (AMR) AF: 0.809 AC: 12368 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4173 AN: 5162

South Asian (SAS) AF: 0.853 AC: 4107 AN: 4814

European-Finnish (FIN) AF: 0.908 AC: 9626 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.939 AC: 63836 AN: 68006

Other (OTH) AF: 0.850 AC: 1796 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.37
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1398193; hg19: chr18-45987139;