rs16862782

chr3-187970102-C-A

Variant summary

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

The NR_135538.1(LINC01991):n.83-2893G>T 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 0.131 in 152,200 control chromosomes in the GnomAD database, including 1,561 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 0.13 (1561 hom., cov: 32)
• Consequence: LINC01991 NR_135538.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473

Genes affected

LINC01991 (HGNC:52823): (long intergenic non-protein coding RNA 1991)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01991	NR_135538.1	n.83-2893G>T		intron_variant, non_coding_transcript_variant
LINC01991	NR_135537.1	n.83-2893G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01991	ENST00000446091.1	n.83-2893G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19968 AN: 152082 Hom.: 1561 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.131 AC: 19977 AN: 152200 Hom.: 1561 Cov.: 32 AF XY: 0.135 AC XY: 10014 AN XY: 74420

Gnomad4 AFR AF: 0.0452

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.165

Alfa AF: 0.163 Hom.: 2788

Bravo AF: 0.126

Asia WGS AF: 0.135 AC: 466 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.6
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16862782; hg19: chr3-187687890;