ENST00000663460.1:n.216+13847C>T

Variant names:

• chr5-152389060-C-T
• rs10515663
• ENST00000663460.1:n.216+13847C>T

Variant summary

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

The ENST00000663460.1(ENSG00000286749):​n.216+13847C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,024 control chromosomes in the GnomAD database, including 2,078 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 0.14 (2078 hom., cov: 32)
• Consequence: ENSG00000286749 ENST00000663460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 5 publications found

Genes affected

ENSG00000286749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 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
ENSG00000286749	ENST00000663460.1	n.216+13847C>T		intron_variant	Intron 1 of 3
ENSG00000286749	ENST00000663819.1	n.183+13847C>T		intron_variant	Intron 1 of 3
ENSG00000286749	ENST00000812686.1	n.87+13847C>T		intron_variant	Intron 1 of 4
ENSG00000286749	ENST00000812687.1	n.185+13847C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22005 AN: 151906 Hom.: 2081 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.145 AC: 21994 AN: 152024 Hom.: 2078 Cov.: 32 AF XY: 0.145 AC XY: 10797 AN XY: 74312

African (AFR) AF: 0.0421 AC: 1749 AN: 41504

American (AMR) AF: 0.237 AC: 3607 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3468

East Asian (EAS) AF: 0.0347 AC: 180 AN: 5184

South Asian (SAS) AF: 0.177 AC: 852 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1934 AN: 10578

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12660 AN: 67922

Other (OTH) AF: 0.142 AC: 300 AN: 2110

Alfa AF: 0.106 Hom.: 294

Bravo AF: 0.147

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10515663; hg19: chr5-151768621;