rs7245959

Variant names:

• chr19-30888202-T-C
• rs7245959
• ENST00000716200.1:n.216-18212T>C

Variant summary

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

The ENST00000716200.1(LINC01834):​n.216-18212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,068 control chromosomes in the GnomAD database, including 12,317 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 0.39 (12317 hom., cov: 32)
• Consequence: LINC01834 ENST00000716200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 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	ENST00000716200.1	n.216-18212T>C		intron_variant	Intron 1 of 2
LINC01834	ENST00000716201.1	n.666+15654T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59642 AN: 151950 Hom.: 12306 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.392 AC: 59670 AN: 152068 Hom.: 12317 Cov.: 32 AF XY: 0.399 AC XY: 29630 AN XY: 74318

African (AFR) AF: 0.284 AC: 11760 AN: 41476

American (AMR) AF: 0.392 AC: 5990 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3170 AN: 5172

South Asian (SAS) AF: 0.564 AC: 2720 AN: 4826

European-Finnish (FIN) AF: 0.459 AC: 4842 AN: 10552

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28210 AN: 67978

Other (OTH) AF: 0.443 AC: 936 AN: 2112

Alfa AF: 0.401 Hom.: 4707

Bravo AF: 0.383

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7245959; hg19: chr19-31379109;