16-86288853-T-C

Variant names:

• chr16-86288853-T-C
• rs987052
• ENST00000599486.1:n.124-1812T>C

Variant summary

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

The ENST00000599486.1(LINC02135):​n.124-1812T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,078 control chromosomes in the GnomAD database, including 4,734 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 0.23 (4734 hom., cov: 32)
• Consequence: LINC02135 ENST00000599486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 9 publications found

Genes affected

LINC02135 (HGNC:27094): (long intergenic non-protein coding RNA 2135)

LINC01081 (HGNC:49124): (long intergenic non-protein coding RNA 1081)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02135	NR_038438.1	n.120-1812T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02135	ENST00000599486.1	n.124-1812T>C		intron_variant	Intron 1 of 2	1
LINC01081	ENST00000597373.2	n.132+12319A>G		intron_variant	Intron 1 of 5	5
LINC01081	ENST00000806422.1	n.280-13031A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35078 AN: 151960 Hom.: 4712 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.231 AC: 35146 AN: 152078 Hom.: 4734 Cov.: 32 AF XY: 0.240 AC XY: 17844 AN XY: 74350

African (AFR) AF: 0.282 AC: 11718 AN: 41480

American (AMR) AF: 0.323 AC: 4933 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2620 AN: 5146

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4828

European-Finnish (FIN) AF: 0.265 AC: 2801 AN: 10586

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10579 AN: 67972

Other (OTH) AF: 0.223 AC: 470 AN: 2112

Alfa AF: 0.192 Hom.: 6269

Bravo AF: 0.242

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.62
DANN	Benign	0.62
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs987052; hg19: chr16-86322459;