rs10041184

Variant names:

• chr5-175080228-G-A
• rs10041184
• ENST00000798224.1:n.56+26068C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-175080228-G-A
• chr5-175080228-G-C
• chr5-175080228-G-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+26068C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,538 control chromosomes in the GnomAD database, including 12,149 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 0.34 (12149 hom., cov: 31)
• Consequence: LINC01951 ENST00000798224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.86

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 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+26068C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52001 AN: 151420 Hom.: 12110 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.344 AC: 52098 AN: 151538 Hom.: 12149 Cov.: 31 AF XY: 0.345 AC XY: 25510 AN XY: 74000

African (AFR) AF: 0.650 AC: 26825 AN: 41300

American (AMR) AF: 0.311 AC: 4732 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3468

East Asian (EAS) AF: 0.569 AC: 2903 AN: 5102

South Asian (SAS) AF: 0.334 AC: 1594 AN: 4768

European-Finnish (FIN) AF: 0.182 AC: 1915 AN: 10508

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12467 AN: 67866

Other (OTH) AF: 0.320 AC: 673 AN: 2106

Alfa AF: 0.242 Hom.: 15616

Bravo AF: 0.370

Asia WGS AF: 0.474 AC: 1646 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.40
PhyloP100		-6.9

Splicing

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

Publications

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Other links and lift over

dbSNP: rs10041184; hg19: chr5-174507231;