15-46685450-C-T

Variant names:

• chr15-46685450-C-T
• rs484525
• ENST00000686120.1:n.192-45792C>T

Variant summary

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

The ENST00000686120.1(ENSG00000287704):​n.192-45792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,726 control chromosomes in the GnomAD database, including 38,556 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 0.71 (38556 hom., cov: 30)
• Consequence: ENSG00000287704 ENST00000686120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 2 publications found

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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
ENSG00000287704	ENST00000686120.1	n.192-45792C>T		intron_variant	Intron 2 of 2
ENSG00000287704	ENST00000736459.1	n.182-45792C>T		intron_variant	Intron 2 of 3
ENSG00000287704	ENST00000736460.1	n.174-45792C>T		intron_variant	Intron 2 of 4
ENSG00000287704	ENST00000736461.1	n.136-45792C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106856 AN: 151608 Hom.: 38501 Cov.: 30

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.705 AC: 106970 AN: 151726 Hom.: 38556 Cov.: 30 AF XY: 0.699 AC XY: 51815 AN XY: 74108

African (AFR) AF: 0.856 AC: 35494 AN: 41460

American (AMR) AF: 0.638 AC: 9708 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2438 AN: 3462

East Asian (EAS) AF: 0.831 AC: 4270 AN: 5140

South Asian (SAS) AF: 0.573 AC: 2752 AN: 4806

European-Finnish (FIN) AF: 0.562 AC: 5903 AN: 10504

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44179 AN: 67824

Other (OTH) AF: 0.672 AC: 1416 AN: 2108

Alfa AF: 0.680 Hom.: 4175

Bravo AF: 0.719

Asia WGS AF: 0.691 AC: 2393 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.5
DANN	Benign	0.51
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs484525; hg19: chr15-46977648;