rs6445035

Positions:

• chr3-165762312-G-A

Variant summary

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

The ENST00000651449.1(LINC01322):​n.1008-83580G>A 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 0.185 in 151,902 control chromosomes in the GnomAD database, including 2,583 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 0.19 (2583 hom., cov: 32)
• Consequence: LINC01322 ENST00000651449.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000651449.1	n.1008-83580G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28112 AN: 151786 Hom.: 2582 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.185 AC: 28113 AN: 151902 Hom.: 2583 Cov.: 32 AF XY: 0.183 AC XY: 13602 AN XY: 74254

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.183

Alfa AF: 0.188 Hom.: 405

Bravo AF: 0.187

Asia WGS AF: 0.142 AC: 497 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6445035; hg19: chr3-165480100;