chr3-187969286-A-C

Position:

• chr3-187969286-A-C

Variant summary

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

The NR_135538.1(LINC01991):​n.83-2077T>G 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 0.388 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 NR_135538.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01991	NR_135538.1	n.83-2077T>G		intron_variant, non_coding_transcript_variant
LINC01991	NR_135537.1	n.83-2077T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01991	ENST00000446091.1	n.83-2077T>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.412

Alfa AF: 0.385 Hom.: 26366

Bravo AF: 0.390

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9820070; hg19: chr3-187687074;