rs2912522

Variant names:

• chr8-69080145-G-A
• rs2912522
• ENST00000518540.5:n.194-11596C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-69080145-G-A
• chr8-69080145-G-T

Variant summary

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

The ENST00000518540.5(LINC01592):​n.194-11596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,010 control chromosomes in the GnomAD database, including 40,448 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 0.73 (40448 hom., cov: 31)
• Consequence: LINC01592 ENST00000518540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 14 publications found

Genes affected

LINC01592 (HGNC:51557): (long intergenic non-protein coding RNA 1592)

ENSG00000308759 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01592	NR_039986.1	n.194-11596C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01592	ENST00000518540.5	n.194-11596C>T		intron_variant	Intron 1 of 4	2
LINC01592	ENST00000664220.1	n.246-11596C>T		intron_variant	Intron 1 of 1
LINC01592	ENST00000836182.1	n.419-11596C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110439 AN: 151892 Hom.: 40408 Cov.: 31

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.727 AC: 110537 AN: 152010 Hom.: 40448 Cov.: 31 AF XY: 0.726 AC XY: 53910 AN XY: 74306

African (AFR) AF: 0.756 AC: 31334 AN: 41464

American (AMR) AF: 0.636 AC: 9724 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2534 AN: 3468

East Asian (EAS) AF: 0.605 AC: 3094 AN: 5114

South Asian (SAS) AF: 0.650 AC: 3129 AN: 4814

European-Finnish (FIN) AF: 0.770 AC: 8155 AN: 10586

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.738 AC: 50168 AN: 67972

Other (OTH) AF: 0.712 AC: 1500 AN: 2108

Alfa AF: 0.730 Hom.: 184563

Bravo AF: 0.720

Asia WGS AF: 0.649 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	16
DANN	Benign	0.59
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2912522; hg19: chr8-69992380;