18-4487509-C-T

Variant names:

• chr18-4487509-C-T
• rs1395204
• ENST00000752337.1:n.313-21578C>T

Variant summary

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

The ENST00000752337.1(ENSG00000297987):​n.313-21578C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 138,890 control chromosomes in the GnomAD database, including 13,457 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 0.45 (13457 hom., cov: 27)
• Consequence: ENSG00000297987 ENST00000752337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 2 publications found

Genes affected

ENSG00000297987 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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
ENSG00000297987	ENST00000752337.1	n.313-21578C>T		intron_variant	Intron 2 of 2
ENSG00000298033	ENST00000752583.1	n.292-569G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.455 AC: 63075 AN: 138764 Hom.: 13437 Cov.: 27

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.455 AC: 63146 AN: 138890 Hom.: 13457 Cov.: 27 AF XY: 0.455 AC XY: 30825 AN XY: 67694

African (AFR) AF: 0.590 AC: 22970 AN: 38932

American (AMR) AF: 0.350 AC: 4637 AN: 13250

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1043 AN: 3174

East Asian (EAS) AF: 0.389 AC: 1791 AN: 4600

South Asian (SAS) AF: 0.316 AC: 1346 AN: 4262

European-Finnish (FIN) AF: 0.514 AC: 5024 AN: 9766

Middle Eastern (MID) AF: 0.295 AC: 69 AN: 234

European-Non Finnish (NFE) AF: 0.404 AC: 25042 AN: 61988

Other (OTH) AF: 0.404 AC: 742 AN: 1836

Alfa AF: 0.366 Hom.: 5524

Bravo AF: 0.425

Asia WGS AF: 0.368 AC: 1273 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1395204; hg19: chr18-4487509;