16-86288853-T-C

Position:

• chr16-86288853-T-C

Variant summary

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

The NR_038438.1(LINC02135):​n.120-1812T>C 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 0.231 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 NR_038438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02135	NR_038438.1	n.120-1812T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01081	ENST00000597373.2	n.132+12319A>G		intron_variant, non_coding_transcript_variant		5
LINC02135	ENST00000599486.1	n.124-1812T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.223

Alfa AF: 0.174 Hom.: 3134

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987052; hg19: chr16-86322459;