2-2922241-G-A

Variant names:

• chr2-2922241-G-A
• rs17491951
• ENST00000457478.1:n.595-24937C>T

Variant summary

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

The ENST00000457478.1(LINC01250):​n.595-24937C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,094 control chromosomes in the GnomAD database, including 6,002 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 0.25 (6002 hom., cov: 32)
• Consequence: LINC01250 ENST00000457478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 4 publications found

Genes affected

LINC01250 (HGNC:49844): (long intergenic non-protein coding RNA 1250)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01250	NR_110228.1	n.595-24937C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01250	ENST00000457478.1	n.595-24937C>T		intron_variant	Intron 5 of 6	2
LINC01250	ENST00000667683.1	n.228-24937C>T		intron_variant	Intron 3 of 4
LINC01250	ENST00000740420.1	n.648-24937C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37593 AN: 151974 Hom.: 6002 Cov.: 32

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.247 AC: 37586 AN: 152094 Hom.: 6002 Cov.: 32 AF XY: 0.247 AC XY: 18342 AN XY: 74346

African (AFR) AF: 0.0625 AC: 2596 AN: 41524

American (AMR) AF: 0.245 AC: 3751 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 762 AN: 3472

East Asian (EAS) AF: 0.116 AC: 601 AN: 5160

South Asian (SAS) AF: 0.165 AC: 791 AN: 4802

European-Finnish (FIN) AF: 0.342 AC: 3613 AN: 10572

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24425 AN: 67962

Other (OTH) AF: 0.234 AC: 494 AN: 2112

Alfa AF: 0.285 Hom.: 10794

Bravo AF: 0.231

Asia WGS AF: 0.129 AC: 449 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	0.022
DANN	Benign	0.47
PhyloP100		-1.9
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: rs17491951; hg19: chr2-2926013;