ENST00000515337.1:n.746-5395T>A

Variant names:

• chr5-159342121-T-A
• rs13188370
• ENST00000515337.1:n.746-5395T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000515337.1(ENSG00000249738):​n.746-5395T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,248 control chromosomes in the GnomAD database, including 64 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 0.024 (64 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

Genes affected

ENSG00000249738 (HGNC:58156):

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0237 (3614/152248) while in subpopulation NFE AF= 0.0351 (2384/68004). AF 95% confidence interval is 0.0339. There are 64 homozygotes in gnomad4. There are 1771 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC285626	NR_037889.1	n.746-5395T>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.746-5395T>A		intron_variant	Intron 2 of 4	2
ENSG00000249738	ENST00000641150.1	n.325-5395T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3614 AN: 152130 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.00710

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00372

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0237 AC: 3614 AN: 152248 Hom.: 64 Cov.: 32 AF XY: 0.0238 AC XY: 1771 AN XY: 74450

Gnomad4 AFR AF: 0.00708

Gnomad4 AMR AF: 0.0281

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00372

Gnomad4 FIN AF: 0.0299

Gnomad4 NFE AF: 0.0351

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0271 Hom.: 8

Bravo AF: 0.0237

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.13
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13188370; hg19: chr5-158769129;