chr8-111395913-G-C

Variant names:

• chr8-111395913-G-C
• rs10505162
• ENST00000521753.5:n.268+15221G>C

Variant summary

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

The ENST00000521753.5(LINC02237):​n.268+15221G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 150,734 control chromosomes in the GnomAD database, including 14,400 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 0.40 (14400 hom., cov: 32)
• Consequence: LINC02237 ENST00000521753.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 1 publications found

Genes affected

LINC02237 (HGNC:53108): (long intergenic non-protein coding RNA 2237)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02237	NR_146282.1	n.117+8171G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02237	ENST00000521753.5	n.268+15221G>C		intron_variant	Intron 2 of 4	3
LINC02237	ENST00000521904.5	n.117+8171G>C		intron_variant	Intron 2 of 3	3
LINC02237	ENST00000832138.1	n.58+19203G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 60779 AN: 150618 Hom.: 14408 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.403 AC: 60786 AN: 150734 Hom.: 14400 Cov.: 32 AF XY: 0.398 AC XY: 29327 AN XY: 73682

African (AFR) AF: 0.168 AC: 6805 AN: 40400

American (AMR) AF: 0.386 AC: 5875 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3468

East Asian (EAS) AF: 0.132 AC: 683 AN: 5172

South Asian (SAS) AF: 0.314 AC: 1511 AN: 4812

European-Finnish (FIN) AF: 0.512 AC: 5377 AN: 10500

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37258 AN: 67858

Other (OTH) AF: 0.414 AC: 866 AN: 2090

Alfa AF: 0.317 Hom.: 913

Bravo AF: 0.385

Asia WGS AF: 0.232 AC: 807 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.49
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs10505162; hg19: chr8-112408142;