8-116339735-G-T

Variant names:

• chr8-116339735-G-T
• rs2316692
• ENST00000835235.1:n.363+45152C>A

Variant summary

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

The ENST00000835235.1(LINC00536):​n.363+45152C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 151,736 control chromosomes in the GnomAD database, including 2,164 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 0.15 (2164 hom., cov: 32)
• Consequence: LINC00536 ENST00000835235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.71
• Publications: 5 publications found

Genes affected

LINC00536 (HGNC:43645): (long intergenic non-protein coding RNA 536)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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
LINC00536	ENST00000835235.1	n.363+45152C>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23051 AN: 151634 Hom.: 2148 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.152 AC: 23108 AN: 151736 Hom.: 2164 Cov.: 32 AF XY: 0.153 AC XY: 11356 AN XY: 74142

African (AFR) AF: 0.257 AC: 10655 AN: 41380

American (AMR) AF: 0.103 AC: 1565 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3472

East Asian (EAS) AF: 0.122 AC: 630 AN: 5162

South Asian (SAS) AF: 0.0816 AC: 392 AN: 4806

European-Finnish (FIN) AF: 0.161 AC: 1680 AN: 10416

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7405 AN: 67934

Other (OTH) AF: 0.139 AC: 291 AN: 2096

Alfa AF: 0.118 Hom.: 4335

Bravo AF: 0.155

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.28
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs2316692; hg19: chr8-117351973;