rs17056705

Variant names:

• chr5-159342245-G-A
• rs17056705
• ENST00000515337.1:n.746-5271G>A

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.746-5271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 152,236 control chromosomes in the GnomAD database, including 585 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 0.079 (585 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 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.746-5271G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249738	ENST00000515337.1	TSL:2	n.746-5271G>A		intron	N/A
	ENSG00000249738	ENST00000641150.1		n.325-5271G>A		intron	N/A
	ENSG00000249738	ENST00000764988.1		n.566+9242G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 11945 AN: 152118 Hom.: 584 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.0785 AC: 11951 AN: 152236 Hom.: 585 Cov.: 32 AF XY: 0.0788 AC XY: 5866 AN XY: 74422

African (AFR) AF: 0.129 AC: 5354 AN: 41518

American (AMR) AF: 0.0576 AC: 881 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 283 AN: 3472

East Asian (EAS) AF: 0.128 AC: 662 AN: 5184

South Asian (SAS) AF: 0.138 AC: 667 AN: 4824

European-Finnish (FIN) AF: 0.0511 AC: 542 AN: 10598

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0481 AC: 3269 AN: 68024

Other (OTH) AF: 0.0876 AC: 185 AN: 2112

Alfa AF: 0.0623 Hom.: 655

Bravo AF: 0.0812

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.59
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs17056705; hg19: chr5-158769253;