chr15-25466064-C-G

Variant names:

• chr15-25466064-C-G
• rs969860
• ENST00000665366.1:n.697-9594G>C

Variant summary

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

The ENST00000665366.1(LINC02250):​n.697-9594G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,238 control chromosomes in the GnomAD database, including 1,038 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 0.11 (1038 hom., cov: 33)
• Consequence: LINC02250 ENST00000665366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 2 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02250	NR_187215.1	n.697-9594G>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02250	ENST00000665366.1	n.697-9594G>C		intron_variant	Intron 4 of 4
LINC02250	ENST00000826796.1	n.499-9594G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16936 AN: 152120 Hom.: 1040 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0931

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.111 AC: 16936 AN: 152238 Hom.: 1038 Cov.: 33 AF XY: 0.107 AC XY: 7967 AN XY: 74422

African (AFR) AF: 0.137 AC: 5699 AN: 41554

American (AMR) AF: 0.0862 AC: 1319 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4820

European-Finnish (FIN) AF: 0.0619 AC: 657 AN: 10606

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 7989 AN: 67982

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.106 Hom.: 114

Bravo AF: 0.113

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.6
DANN	Benign	0.88
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs969860; hg19: chr15-25711211;