rs10516125

Variant names:

• chr5-175053830-A-G
• rs10516125
• ENST00000798224.1:n.56+52466T>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000798224.1(LINC01951):​n.56+52466T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0211 in 152,298 control chromosomes in the GnomAD database, including 72 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 0.021 (72 hom., cov: 32)
• Consequence: LINC01951 ENST00000798224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.54
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0754 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+52466T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3207 AN: 152180 Hom.: 69 Cov.: 32

Gnomad AFR AF: 0.0148

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0793

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0211 AC: 3218 AN: 152298 Hom.: 72 Cov.: 32 AF XY: 0.0222 AC XY: 1653 AN XY: 74470

African (AFR) AF: 0.0147 AC: 613 AN: 41568

American (AMR) AF: 0.0792 AC: 1211 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3468

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4816

European-Finnish (FIN) AF: 0.0120 AC: 127 AN: 10612

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0156 AC: 1060 AN: 68026

Other (OTH) AF: 0.0269 AC: 57 AN: 2116

Alfa AF: 0.0202 Hom.: 40

Bravo AF: 0.0247

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	23
DANN	Benign	0.90
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs10516125; hg19: chr5-174480833;