3-187969286-A-C

Variant names:

• chr3-187969286-A-C
• rs9820070
• ENST00000446091.1:n.83-2077T>G

Variant summary

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

The ENST00000446091.1(LINC01991):​n.83-2077T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,452 control chromosomes in the GnomAD database, including 11,612 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 0.39 (11612 hom., cov: 30)
• Consequence: LINC01991 ENST00000446091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 21 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446091.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01991	NR_135537.1		n.83-2077T>G		intron	N/A
	LINC01991	NR_135538.1		n.83-2077T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01991	ENST00000446091.1	TSL:2	n.83-2077T>G		intron	N/A
	LINC01991	ENST00000744770.1		n.840-10323T>G		intron	N/A
	LINC01991	ENST00000744771.1		n.828-10323T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58749 AN: 151336 Hom.: 11596 Cov.: 30

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.388 AC: 58814 AN: 151452 Hom.: 11612 Cov.: 30 AF XY: 0.383 AC XY: 28351 AN XY: 73964

African (AFR) AF: 0.414 AC: 17049 AN: 41198

American (AMR) AF: 0.340 AC: 5177 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3466

East Asian (EAS) AF: 0.349 AC: 1799 AN: 5150

South Asian (SAS) AF: 0.246 AC: 1184 AN: 4822

European-Finnish (FIN) AF: 0.374 AC: 3884 AN: 10384

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26663 AN: 67892

Other (OTH) AF: 0.412 AC: 869 AN: 2110

Alfa AF: 0.386 Hom.: 52529

Bravo AF: 0.390

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs9820070; hg19: chr3-187687074;