rs73371737

Variant names:

• chr15-25539629-C-A
• rs73371737
• ENST00000422117.1:n.168-31423G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-25539629-C-A
• chr15-25539629-C-T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422117.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02250	NR_187214.1		n.183-22984G>T		intron	N/A
	LINC02250	NR_187215.1		n.183-22984G>T		intron	N/A
	LINC02250	NR_187216.1		n.183-31423G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02250	ENST00000422117.1	TSL:1	n.168-31423G>T		intron	N/A
	LINC02250	ENST00000651932.1		n.183-22984G>T		intron	N/A
	LINC02250	ENST00000655390.2		n.190-22984G>T		intron	N/A

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

African (AFR) AF: 0.255 AC: 10548 AN: 41442

American (AMR) AF: 0.0826 AC: 1262 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0969 AC: 336 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5172

South Asian (SAS) AF: 0.0904 AC: 436 AN: 4824

European-Finnish (FIN) AF: 0.0691 AC: 731 AN: 10578

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6763 AN: 67984

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.101 Hom.: 1539

Bravo AF: 0.138

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.17
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs73371737; hg19: chr15-25784776;