ENST00000765258.1:n.251-613C>T

Variant names:

• chr5-36445700-C-T
• rs17358298
• ENST00000765258.1:n.251-613C>T

Variant summary

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

The ENST00000765258.1(ENSG00000299633):​n.251-613C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,196 control chromosomes in the GnomAD database, including 975 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 0.10 (975 hom., cov: 33)
• Consequence: ENSG00000299633 ENST00000765258.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 3 publications found

Genes affected

ENSG00000299633 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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
ENSG00000299633	ENST00000765258.1	n.251-613C>T		intron_variant	Intron 2 of 2
ENSG00000299633	ENST00000765259.1	n.153-613C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15256 AN: 152078 Hom.: 975 Cov.: 33

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.100 AC: 15255 AN: 152196 Hom.: 975 Cov.: 33 AF XY: 0.0977 AC XY: 7271 AN XY: 74400

African (AFR) AF: 0.0334 AC: 1386 AN: 41552

American (AMR) AF: 0.100 AC: 1532 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5178

South Asian (SAS) AF: 0.0802 AC: 387 AN: 4826

European-Finnish (FIN) AF: 0.124 AC: 1316 AN: 10584

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9586 AN: 67988

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.128 Hom.: 1183

Bravo AF: 0.0958

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs17358298; hg19: chr5-36445802;