rs10052709

Variant names:

• chr5-159333469-C-G
• rs10052709
• ENST00000515337.1:n.745+466C>G

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.745+466C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,084 control chromosomes in the GnomAD database, including 1,737 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 0.15 (1737 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 18 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	NR_037889.1	n.745+466C>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.745+466C>G		intron_variant	Intron 2 of 4	2
ENSG00000249738	ENST00000641150.1	n.324+466C>G		intron_variant	Intron 2 of 4
ENSG00000249738	ENST00000764988.1	n.566+466C>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22055 AN: 151966 Hom.: 1739 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.145 AC: 22053 AN: 152084 Hom.: 1737 Cov.: 32 AF XY: 0.139 AC XY: 10321 AN XY: 74348

African (AFR) AF: 0.204 AC: 8455 AN: 41462

American (AMR) AF: 0.108 AC: 1653 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3466

East Asian (EAS) AF: 0.0761 AC: 394 AN: 5178

South Asian (SAS) AF: 0.0541 AC: 261 AN: 4824

European-Finnish (FIN) AF: 0.0770 AC: 814 AN: 10578

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9214 AN: 67974

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.143 Hom.: 226

Bravo AF: 0.153

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.31
DANN	Benign	0.58
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10052709; hg19: chr5-158760477;