chr15-25539629-C-A

Position:

• chr15-25539629-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422117.1(LINC02250):​n.168-31423G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,062 control chromosomes in the GnomAD database, including 1,803 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 0.13 (1803 hom., cov: 32)
• Consequence: LINC02250 ENST00000422117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

LINC02250 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02250	NR_187214.1	n.183-22984G>T		intron_variant
LINC02250	NR_187215.1	n.183-22984G>T		intron_variant
LINC02250	NR_187216.1	n.183-31423G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02250	ENST00000422117.1	n.168-31423G>T		intron_variant		1
LINC02250	ENST00000651932.1	n.183-22984G>T		intron_variant
LINC02250	ENST00000655390.1	n.183-22984G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20391 AN: 151944 Hom.: 1800 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.0969

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0911

Gnomad FIN AF: 0.0691

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.134 AC: 20411 AN: 152062 Hom.: 1803 Cov.: 32 AF XY: 0.131 AC XY: 9762 AN XY: 74340

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.0969

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0904

Gnomad4 FIN AF: 0.0691

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0764 Hom.: 159

Bravo AF: 0.138

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73371737; hg19: chr15-25784776;