18-48461304-T-G

Variant names:

• chr18-48461304-T-G
• rs1877412
• ENST00000751899.1:n.338+20762A>C

Variant summary

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

The ENST00000751899.1(ENSG00000297938):​n.338+20762A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,228 control chromosomes in the GnomAD database, including 57,603 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 0.87 (57603 hom., cov: 32)
• Consequence: ENSG00000297938 ENST00000751899.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 3 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=-0.98).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297938	ENST00000751899.1	n.338+20762A>C		intron_variant	Intron 5 of 5
ENSG00000297938	ENST00000751900.1	n.281+21787A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131757 AN: 152110 Hom.: 57560 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.866 AC: 131856 AN: 152228 Hom.: 57603 Cov.: 32 AF XY: 0.863 AC XY: 64250 AN XY: 74444

African (AFR) AF: 0.754 AC: 31298 AN: 41498

American (AMR) AF: 0.825 AC: 12610 AN: 15292

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

East Asian (EAS) AF: 0.808 AC: 4177 AN: 5170

South Asian (SAS) AF: 0.875 AC: 4226 AN: 4832

European-Finnish (FIN) AF: 0.908 AC: 9629 AN: 10604

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

European-Non Finnish (NFE) AF: 0.939 AC: 63914 AN: 68038

Other (OTH) AF: 0.872 AC: 1845 AN: 2116

Alfa AF: 0.906 Hom.: 31600

Bravo AF: 0.854

Asia WGS AF: 0.865 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.44
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1877412; hg19: chr18-45987675;