chr3-165714691-C-T

Variant names:

• chr3-165714691-C-T
• rs1071526
• ENST00000651449.1:n.1007+60496C>T

Variant summary

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

The ENST00000651449.1(LINC01322):​n.1007+60496C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000651449.1	n.1007+60496C>T		intron_variant	Intron 8 of 8

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

African (AFR) AF: 0.292 AC: 12123 AN: 41472

American (AMR) AF: 0.189 AC: 2884 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3468

East Asian (EAS) AF: 0.116 AC: 603 AN: 5180

South Asian (SAS) AF: 0.177 AC: 854 AN: 4820

European-Finnish (FIN) AF: 0.0631 AC: 668 AN: 10590

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8992 AN: 67966

Other (OTH) AF: 0.190 AC: 401 AN: 2112

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1071526; hg19: chr3-165432479;