rs2605463

Variant names:

• chr15-25569304-A-G
• rs2605463
• ENST00000422117.1:n.167+9321T>C

Variant summary

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

The ENST00000422117.1(LINC02250):​n.167+9321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,086 control chromosomes in the GnomAD database, including 22,938 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 0.52 (22938 hom., cov: 32)
• Consequence: LINC02250 ENST00000422117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 3 publications found

Genes affected

LINC02250 (HGNC:53148): (long intergenic non-protein coding RNA 2250)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02250	NR_187214.1	n.182+9321T>C		intron_variant	Intron 1 of 6
LINC02250	NR_187215.1	n.182+9321T>C		intron_variant	Intron 1 of 4
LINC02250	NR_187216.1	n.182+9321T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02250	ENST00000422117.1	n.167+9321T>C		intron_variant	Intron 1 of 3	1
LINC02250	ENST00000651932.1	n.182+9321T>C		intron_variant	Intron 1 of 6
LINC02250	ENST00000655390.2	n.189+9321T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79045 AN: 151968 Hom.: 22933 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.520 AC: 79052 AN: 152086 Hom.: 22938 Cov.: 32 AF XY: 0.522 AC XY: 38811 AN XY: 74354

African (AFR) AF: 0.232 AC: 9631 AN: 41504

American (AMR) AF: 0.599 AC: 9168 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3803 AN: 5160

South Asian (SAS) AF: 0.616 AC: 2965 AN: 4814

European-Finnish (FIN) AF: 0.615 AC: 6491 AN: 10546

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.632 AC: 42971 AN: 67980

Other (OTH) AF: 0.544 AC: 1149 AN: 2114

Alfa AF: 0.593 Hom.: 88375

Bravo AF: 0.507

Asia WGS AF: 0.629 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2605463; hg19: chr15-25814451;