rs10425253

Variant names:

• chr19-30855628-G-A
• rs10425253
• ENST00000585364.1:n.106+4548G>A

Variant summary

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

The ENST00000585364.1(LINC01834):​n.106+4548G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,148 control chromosomes in the GnomAD database, including 3,914 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 0.21 (3914 hom., cov: 33)
• Consequence: LINC01834 ENST00000585364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 2 publications found

Genes affected

LINC01834 (HGNC:52648): (long intergenic non-protein coding RNA 1834)

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 (NFE) allele frequency at 95% confidence interval = 0.278 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
LINC01834	ENST00000585364.1	n.106+4548G>A		intron_variant	Intron 1 of 1	4
LINC01834	ENST00000716200.1	n.216-50786G>A		intron_variant	Intron 1 of 2
LINC01834	ENST00000716201.1	n.165-16419G>A		intron_variant	Intron 1 of 3
LINC01834	ENST00000824349.1	n.131-16419G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32387 AN: 152030 Hom.: 3912 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.213 AC: 32397 AN: 152148 Hom.: 3914 Cov.: 33 AF XY: 0.204 AC XY: 15172 AN XY: 74384

African (AFR) AF: 0.163 AC: 6755 AN: 41522

American (AMR) AF: 0.155 AC: 2375 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3472

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5174

South Asian (SAS) AF: 0.0763 AC: 368 AN: 4824

European-Finnish (FIN) AF: 0.203 AC: 2143 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19094 AN: 67978

Other (OTH) AF: 0.184 AC: 387 AN: 2108

Alfa AF: 0.254 Hom.: 659

Bravo AF: 0.208

Asia WGS AF: 0.0680 AC: 236 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	2.6
DANN	Benign	0.46
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs10425253; hg19: chr19-31346535;