rs695167

Variant names:

• chr8-69118917-G-A
• rs695167
• ENST00000836182.1:n.419-50368C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-69118917-G-A
• chr8-69118917-G-C

Variant summary

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

The ENST00000836182.1(LINC01592):​n.419-50368C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 150,140 control chromosomes in the GnomAD database, including 32,136 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 0.64 (32136 hom., cov: 31)
• Consequence: LINC01592 ENST00000836182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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
LINC01592	ENST00000836182.1	n.419-50368C>T		intron_variant	Intron 1 of 4
LINC01592	ENST00000836183.1	n.434-50368C>T		intron_variant	Intron 1 of 1
ENSG00000308759	ENST00000836279.1	n.334+408G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.638 AC: 95772 AN: 150038 Hom.: 32086 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.639 AC: 95870 AN: 150140 Hom.: 32136 Cov.: 31 AF XY: 0.645 AC XY: 47270 AN XY: 73312

African (AFR) AF: 0.831 AC: 34170 AN: 41110

American (AMR) AF: 0.649 AC: 9795 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1736 AN: 3436

East Asian (EAS) AF: 0.957 AC: 4902 AN: 5124

South Asian (SAS) AF: 0.702 AC: 3358 AN: 4782

European-Finnish (FIN) AF: 0.599 AC: 6087 AN: 10160

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34078 AN: 67172

Other (OTH) AF: 0.624 AC: 1293 AN: 2072

Alfa AF: 0.557 Hom.: 6051

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.39
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs695167; hg19: chr8-70031152;