rs450443

chr16-85935285-T-G

Variant summary

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

The ENST00000598933.2(LINC02132):n.746A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,982 control chromosomes in the GnomAD database, including 10,498 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 0.35 (10498 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: LINC02132 ENST00000598933.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LINC02132 (HGNC:52992): (long intergenic non-protein coding RNA 2132)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02132	XR_001752391.2	n.697A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02132	ENST00000598933.2	n.746A>C		non_coding_transcript_exon_variant	2/2	2
	ENST00000646214.1	n.78-10131T>G		intron_variant, non_coding_transcript_variant
	ENST00000645383.1	n.393+3011T>G		intron_variant, non_coding_transcript_variant
	ENST00000646986.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53166 AN: 151848 Hom.: 10466 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.214 AC: 3 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.350 AC: 53251 AN: 151968 Hom.: 10498 Cov.: 32 AF XY: 0.353 AC XY: 26207 AN XY: 74292

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.299

Alfa AF: 0.324 Hom.: 1092

Bravo AF: 0.357

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs450443; hg19: chr16-85968891;