5-175082883-G-A

Variant names:

• chr5-175082883-G-A
• rs2381958
• ENST00000798224.1:n.56+23413C>T

Variant summary

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

The ENST00000798224.1(LINC01951):​n.56+23413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,050 control chromosomes in the GnomAD database, including 4,528 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 0.23 (4528 hom., cov: 33)
• Consequence: LINC01951 ENST00000798224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 publications found

Genes affected

LINC01951 (HGNC:52774): (long intergenic non-protein coding RNA 1951)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01951	ENST00000798224.1	n.56+23413C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34646 AN: 151932 Hom.: 4522 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.228 AC: 34682 AN: 152050 Hom.: 4528 Cov.: 33 AF XY: 0.231 AC XY: 17141 AN XY: 74304

African (AFR) AF: 0.297 AC: 12332 AN: 41470

American (AMR) AF: 0.256 AC: 3916 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2696 AN: 5148

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4816

European-Finnish (FIN) AF: 0.164 AC: 1733 AN: 10566

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11425 AN: 67986

Other (OTH) AF: 0.225 AC: 476 AN: 2116

Alfa AF: 0.185 Hom.: 1489

Bravo AF: 0.242

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2381958; hg19: chr5-174509886;