5-159342121-T-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	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
ENSG00000249738	ENST00000764988.1	n.566+9118T>A		intron_variant	Intron 2 of 6

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

African (AFR) AF: 0.00708 AC: 294 AN: 41550

American (AMR) AF: 0.0281 AC: 430 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5150

South Asian (SAS) AF: 0.00372 AC: 18 AN: 4834

European-Finnish (FIN) AF: 0.0299 AC: 317 AN: 10618

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0351 AC: 2384 AN: 68004

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

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
PhyloP100		-0.98
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13188370; hg19: chr5-158769129;