3-165337681-C-T

Variant names:

• chr3-165337681-C-T
• rs1595781
• ENST00000470138.5:n.201-45114C>T

Variant summary

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

The ENST00000470138.5(LINC01322):​n.201-45114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,784 control chromosomes in the GnomAD database, including 34,117 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 0.66 (34117 hom., cov: 33)
• Consequence: LINC01322 ENST00000470138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01322	NR_125764.2	n.213-36578C>T		intron_variant	Intron 1 of 5
LINC01322	NR_174098.1	n.213-7791C>T		intron_variant	Intron 1 of 6
LINC01322	NR_174099.1	n.213-7791C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000470138.5	n.201-45114C>T		intron_variant	Intron 1 of 3	4
LINC01322	ENST00000494915.2	n.165-7791C>T		intron_variant	Intron 1 of 4	4
LINC01322	ENST00000498616.7	n.203-7791C>T		intron_variant	Intron 1 of 6	4

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100442 AN: 151666 Hom.: 34095 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.662 AC: 100497 AN: 151784 Hom.: 34117 Cov.: 33 AF XY: 0.664 AC XY: 49228 AN XY: 74144

African (AFR) AF: 0.563 AC: 23325 AN: 41460

American (AMR) AF: 0.630 AC: 9583 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2421 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4423 AN: 5150

South Asian (SAS) AF: 0.797 AC: 3846 AN: 4828

European-Finnish (FIN) AF: 0.671 AC: 7050 AN: 10500

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47735 AN: 67878

Other (OTH) AF: 0.661 AC: 1383 AN: 2092

Alfa AF: 0.647 Hom.: 13825

Bravo AF: 0.646

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.62
DANN	Benign	0.64
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1595781; hg19: chr3-165055469;