rs1212084

chr3-165714691-C-T

Variant summary

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

The ENST00000651449.1(LINC01322):n.1007+60496C>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 0.179 in 152,080 control chromosomes in the GnomAD database, including 2,845 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 0.18 (2845 hom., cov: 32)
• Consequence: LINC01322 ENST00000651449.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271

Genes affected

LINC01322 (HGNC:50528): (long intergenic non-protein coding RNA 1322)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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
LINC01322	ENST00000651449.1	n.1007+60496C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27102 AN: 151962 Hom.: 2834 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0631

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.179 AC: 27157 AN: 152080 Hom.: 2845 Cov.: 32 AF XY: 0.176 AC XY: 13063 AN XY: 74374

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0631

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.190

Alfa AF: 0.153 Hom.: 259

Bravo AF: 0.193

Asia WGS AF: 0.165 AC: 571 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	8.0
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1071526; hg19: chr3-165432479;