chr19-9830138-C-G

Variant names:

• chr19-9830138-C-G
• rs2287839
• ENST00000731112.1:n.376G>C

Variant summary

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

The ENST00000731112.1(PIN1-DT):​n.376G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 1,199,304 control chromosomes in the GnomAD database, including 6,708 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 0.14 (2368 hom., cov: 32)
  • Exomes 𝑓: 0.074 (4340 hom.)
• Consequence: PIN1-DT ENST00000731112.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 18 publications found

Genes affected

PIN1-DT (HGNC:55303): (PIN1 divergent transcript)

UBL5 (HGNC:13736): (ubiquitin like 5) This gene encodes a member of a group of proteins similar to ubiquitin. The encoded protein is not thought to degrade proteins like ubiquitin but to affect their function through being bound to target proteins by an isopeptide bond. The gene product has been studied as a link to predisposition to obesity based on its expression in Psammomys obesus, the fat sand rat, which is an animal model for obesity studies. Variation in this gene was found to be significantly associated with some metabolic traits (PMID: 15331561) but not associated with childhood obesity (PMID: 19189687). Pseudogenes of this gene are located on chromosomes 3, 5 and 17. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBL5	NM_001048241.3	c.*130C>G		downstream_gene_variant		ENST00000586895.6	NP_001041706.1
UBL5	NM_024292.4	c.*130C>G		downstream_gene_variant			NP_077268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBL5	ENST00000586895.6	c.*130C>G		downstream_gene_variant		1	NM_001048241.3	ENSP00000468656.1
UBL5	ENST00000593087.1	c.*153C>G		downstream_gene_variant		3		ENSP00000467663.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20827 AN: 152050 Hom.: 2358 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.0743 AC: 77764 AN: 1047134 Hom.: 4340 Cov.: 13 AF XY: 0.0758 AC XY: 40048 AN XY: 528294

African (AFR) AF: 0.307 AC: 7617 AN: 24818

American (AMR) AF: 0.134 AC: 4819 AN: 35864

Ashkenazi Jewish (ASJ) AF: 0.0465 AC: 929 AN: 19984

East Asian (EAS) AF: 0.0442 AC: 1623 AN: 36746

South Asian (SAS) AF: 0.161 AC: 10953 AN: 68198

European-Finnish (FIN) AF: 0.0523 AC: 2304 AN: 44084

Middle Eastern (MID) AF: 0.115 AC: 370 AN: 3220

European-Non Finnish (NFE) AF: 0.0588 AC: 45201 AN: 768228

Other (OTH) AF: 0.0858 AC: 3948 AN: 45992

GnomAD4 genome AF: 0.137 AC: 20886 AN: 152170 Hom.: 2368 Cov.: 32 AF XY: 0.137 AC XY: 10181 AN XY: 74392

African (AFR) AF: 0.304 AC: 12618 AN: 41468

American (AMR) AF: 0.112 AC: 1706 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3470

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5186

South Asian (SAS) AF: 0.165 AC: 798 AN: 4828

European-Finnish (FIN) AF: 0.0574 AC: 609 AN: 10608

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4339 AN: 68018

Other (OTH) AF: 0.133 AC: 281 AN: 2112

Alfa AF: 0.108 Hom.: 205

Bravo AF: 0.148

Asia WGS AF: 0.160 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.34
PhyloP100		-0.062
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: rs2287839; hg19: chr19-9940814;