19-47868938-C-T

Variant names:

• chr19-47868938-C-T
• rs182420
• XR_936005.3:n.322+102G>A

Variant summary

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

The XR_936005.3(LINC01595):​n.322+102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,198 control chromosomes in the GnomAD database, including 48,965 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 0.80 (48965 hom., cov: 34)
• Consequence: LINC01595 XR_936005.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44
• Publications: 33 publications found

Genes affected

LINC01595 (HGNC:51586): (long intergenic non-protein coding RNA 1595) Implicated in prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121763 AN: 152080 Hom.: 48923 Cov.: 34

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.801 AC: 121862 AN: 152198 Hom.: 48965 Cov.: 34 AF XY: 0.802 AC XY: 59644 AN XY: 74400

African (AFR) AF: 0.870 AC: 36159 AN: 41544

American (AMR) AF: 0.792 AC: 12088 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2495 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4774 AN: 5182

South Asian (SAS) AF: 0.783 AC: 3779 AN: 4828

European-Finnish (FIN) AF: 0.774 AC: 8187 AN: 10580

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51780 AN: 68014

Other (OTH) AF: 0.801 AC: 1694 AN: 2114

Alfa AF: 0.775 Hom.: 107431

Bravo AF: 0.805

Asia WGS AF: 0.867 AC: 3013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs182420; hg19: chr19-48372195;