18-30098322-C-T

Variant names:

• chr18-30098322-C-T
• rs2418453
• ENST00000729000.1:n.383-10057G>A

Variant summary

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

The ENST00000729000.1(ENSG00000295284):​n.383-10057G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,002 control chromosomes in the GnomAD database, including 7,099 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 0.27 (7099 hom., cov: 32)
• Consequence: ENSG00000295284 ENST00000729000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 1 publications found

Genes affected

ENSG00000295284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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
ENSG00000295284	ENST00000729000.1	n.383-10057G>A		intron_variant	Intron 2 of 3
ENSG00000295284	ENST00000729001.1	n.396+10068G>A		intron_variant	Intron 2 of 2
ENSG00000295284	ENST00000729002.1	n.399-10057G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41802 AN: 151884 Hom.: 7096 Cov.: 32

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.275 AC: 41799 AN: 152002 Hom.: 7099 Cov.: 32 AF XY: 0.278 AC XY: 20632 AN XY: 74312

African (AFR) AF: 0.0879 AC: 3646 AN: 41486

American (AMR) AF: 0.227 AC: 3469 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1717 AN: 5154

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4822

European-Finnish (FIN) AF: 0.433 AC: 4568 AN: 10556

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25128 AN: 67924

Other (OTH) AF: 0.256 AC: 540 AN: 2106

Alfa AF: 0.345 Hom.: 5154

Bravo AF: 0.248

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2418453; hg19: chr18-27678287;