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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371004	XR_001751689.2	n.655-1964G>A		intron_variant	Intron 4 of 9
LOC105371004	XR_001751690.2	n.549-1964G>A		intron_variant	Intron 4 of 9
LOC105371004	XR_001751691.2	n.357-1964G>A		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02253	ENST00000740177.1	n.296-4819C>T		intron_variant	Intron 1 of 6
LINC02253	ENST00000740178.1	n.237-4819C>T		intron_variant	Intron 1 of 5
LINC02253	ENST00000740179.1	n.203-4819C>T		intron_variant	Intron 1 of 6

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 v4.3

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;