rs1450418

Variant names:

• chr15-36874677-C-T
• rs1450418
• ENST00000690156.1:n.385+1683G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000690156.1(ENSG00000259280):​n.385+1683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,050 control chromosomes in the GnomAD database, including 35,137 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 0.67 (35137 hom., cov: 33)
• Consequence: ENSG00000259280 ENST00000690156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.938
• Publications: 3 publications found

Genes affected

ENSG00000259280 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC145845	NR_024264.1	n.687+1683G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259280	ENST00000690156.1	n.385+1683G>A		intron_variant	Intron 3 of 4
ENSG00000259280	ENST00000785414.1	n.587+1683G>A		intron_variant	Intron 4 of 5
ENSG00000259280	ENST00000785415.1	n.613+5085G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102514 AN: 151932 Hom.: 35110 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.675 AC: 102595 AN: 152050 Hom.: 35137 Cov.: 33 AF XY: 0.678 AC XY: 50433 AN XY: 74332

African (AFR) AF: 0.558 AC: 23125 AN: 41432

American (AMR) AF: 0.770 AC: 11765 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2407 AN: 3468

East Asian (EAS) AF: 0.764 AC: 3957 AN: 5180

South Asian (SAS) AF: 0.667 AC: 3220 AN: 4824

European-Finnish (FIN) AF: 0.728 AC: 7693 AN: 10564

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48036 AN: 67986

Other (OTH) AF: 0.703 AC: 1487 AN: 2114

Alfa AF: 0.701 Hom.: 156687

Bravo AF: 0.678

Asia WGS AF: 0.706 AC: 2455 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.72
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs1450418; hg19: chr15-37166878;