rs11170826

Positions:

• chr12-54138168-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652305.1(LINC02381):​n.423-3584T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,288 control chromosomes in the GnomAD database, including 1,421 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 0.13 (1421 hom., cov: 33)
• Consequence: LINC02381 ENST00000652305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57

Genes affected

LINC02381 (HGNC:53304): (long intergenic non-protein coding RNA 2381)

SMUG1 (HGNC:17148): (single-strand-selective monofunctional uracil-DNA glycosylase 1) This gene encodes a protein that participates in base excision repair by removing uracil from single- and double-stranded DNA. Many alternatively spliced transcript variants exist for this gene; the full-length nature is known for some but not all of the variants. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02381	ENST00000652305.1	n.423-3584T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19415 AN: 152170 Hom.: 1417 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.128 AC: 19435 AN: 152288 Hom.: 1421 Cov.: 33 AF XY: 0.126 AC XY: 9373 AN XY: 74468

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.00250

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.125

Alfa AF: 0.109 Hom.: 176

Bravo AF: 0.129

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11170826; hg19: chr12-54531952;