3-169027386-C-T

Variant summary

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

The ENST00000650951.1(LINC01997):n.456-9931C>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 0.0577 in 152,140 control chromosomes in the GnomAD database, including 712 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 0.058 (712 hom., cov: 30)
• Consequence: LINC01997 ENST00000650951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LINC01997 (HGNC:52831): (long intergenic non-protein coding RNA 1997)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01997	ENST00000650951.1	n.456-9931C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8758 AN: 152022 Hom.: 706 Cov.: 30

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0577 AC: 8777 AN: 152140 Hom.: 712 Cov.: 30 AF XY: 0.0612 AC XY: 4553 AN XY: 74384

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0131

Gnomad4 NFE AF: 0.0235

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0625 Hom.: 146

Bravo AF: 0.0732

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.99
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024830; hg19: chr3-168745174;