ENST00000663460.1:n.216+12739T>C

Variant names:

• chr5-152387952-T-C
• rs10515662
• ENST00000663460.1:n.216+12739T>C

Variant summary

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

The ENST00000663460.1(ENSG00000286749):​n.216+12739T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,878 control chromosomes in the GnomAD database, including 2,134 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 0.15 (2134 hom., cov: 32)
• Consequence: ENSG00000286749 ENST00000663460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.233 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+12739T>C		intron_variant	Intron 1 of 3
ENSG00000286749	ENST00000663819.1	n.183+12739T>C		intron_variant	Intron 1 of 3
ENSG00000286749	ENST00000812686.1	n.87+12739T>C		intron_variant	Intron 1 of 4
ENSG00000286749	ENST00000812687.1	n.185+12739T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22952 AN: 151760 Hom.: 2135 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.151 AC: 22953 AN: 151878 Hom.: 2134 Cov.: 32 AF XY: 0.152 AC XY: 11289 AN XY: 74258

African (AFR) AF: 0.0648 AC: 2685 AN: 41464

American (AMR) AF: 0.239 AC: 3643 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3464

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5172

South Asian (SAS) AF: 0.177 AC: 854 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10580

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

European-Non Finnish (NFE) AF: 0.186 AC: 12641 AN: 67818

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.164 Hom.: 331

Bravo AF: 0.155

Asia WGS AF: 0.0870 AC: 302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10515662; hg19: chr5-151767513;