5-159354596-T-C

Variant names:

• chr5-159354596-T-C
• rs6869411
• ENST00000515337.1:n.953+475T>C

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.953+475T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,926 control chromosomes in the GnomAD database, including 15,069 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 0.43 (15069 hom., cov: 31)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515337.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	NR_037889.1		n.953+475T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249738	ENST00000515337.1	TSL:2	n.953+475T>C		intron	N/A
	ENSG00000249738	ENST00000635333.1	TSL:5	n.282+475T>C		intron	N/A
	ENSG00000249738	ENST00000641150.1		n.532+475T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65946 AN: 151808 Hom.: 15047 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.435 AC: 66033 AN: 151926 Hom.: 15069 Cov.: 31 AF XY: 0.442 AC XY: 32810 AN XY: 74230

African (AFR) AF: 0.554 AC: 22959 AN: 41406

American (AMR) AF: 0.444 AC: 6770 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2379 AN: 5164

South Asian (SAS) AF: 0.463 AC: 2231 AN: 4814

European-Finnish (FIN) AF: 0.462 AC: 4869 AN: 10532

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24382 AN: 67966

Other (OTH) AF: 0.399 AC: 840 AN: 2106

Alfa AF: 0.376 Hom.: 43309

Bravo AF: 0.439

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6869411; hg19: chr5-158781604;