rs2912522

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_039986.1(LINC01592):​n.194-11596C>T variant causes a intron, non coding transcript 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 NR_039986.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01592	NR_039986.1	n.194-11596C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01592	ENST00000518540.5	n.194-11596C>T		intron_variant, non_coding_transcript_variant		2
LINC01592	ENST00000664220.1	n.246-11596C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.712

Alfa AF: 0.727 Hom.: 84985

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2912522; hg19: chr8-69992380;