rs11852342

Variant names:

• chr15-97086204-C-T
• rs11852342
• ENST00000740177.1:n.296-4819C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000740177.1(LINC02253):​n.296-4819C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,030 control chromosomes in the GnomAD database, including 160 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 0.043 (160 hom., cov: 32)
• Consequence: LINC02253 ENST00000740177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 0 publications found

Genes affected

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

LOC105371004 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0428 (6514/152030) while in subpopulation NFE AF = 0.0462 (3138/67982). AF 95% confidence interval is 0.0448. There are 160 homozygotes in GnomAd4. There are 3035 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 160 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740177.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02253	ENST00000740177.1		n.296-4819C>T		intron	N/A
	LINC02253	ENST00000740178.1		n.237-4819C>T		intron	N/A
	LINC02253	ENST00000740179.1		n.203-4819C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0427 AC: 6489 AN: 151912 Hom.: 153 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.0453

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0428 AC: 6514 AN: 152030 Hom.: 160 Cov.: 32 AF XY: 0.0408 AC XY: 3035 AN XY: 74328

African (AFR) AF: 0.0446 AC: 1850 AN: 41452

American (AMR) AF: 0.0354 AC: 541 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3470

East Asian (EAS) AF: 0.0434 AC: 224 AN: 5158

South Asian (SAS) AF: 0.0458 AC: 220 AN: 4808

European-Finnish (FIN) AF: 0.0312 AC: 330 AN: 10574

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0462 AC: 3138 AN: 67982

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0456 Hom.: 487

Bravo AF: 0.0432

Asia WGS AF: 0.0670 AC: 232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs11852342; hg19: chr15-97629434;