2-33860541-C-T

Variant names:

• chr2-33860541-C-T
• rs17014226
• ENST00000366209.6:n.134+4788C>T

Variant summary

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

The ENST00000366209.6(LINC01320):​n.134+4788C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 149,950 control chromosomes in the GnomAD database, including 1,717 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 0.11 (1717 hom., cov: 30)
• Consequence: LINC01320 ENST00000366209.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 publications found

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

LINC01317 (HGNC:50523): (long intergenic non-protein coding RNA 1317)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.134+4788C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.134+4788C>T		intron_variant	Intron 2 of 5	5
LINC01320	ENST00000442026.1	n.112+4788C>T		intron_variant	Intron 2 of 6	3
LINC01320	ENST00000667658.1	n.129-2731C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17074 AN: 149836 Hom.: 1719 Cov.: 30

Gnomad AFR AF: 0.0475

Gnomad AMI AF: 0.0683

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.0994

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.114 AC: 17070 AN: 149950 Hom.: 1717 Cov.: 30 AF XY: 0.115 AC XY: 8437 AN XY: 73060

African (AFR) AF: 0.0473 AC: 1921 AN: 40576

American (AMR) AF: 0.107 AC: 1616 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3460

East Asian (EAS) AF: 0.596 AC: 3028 AN: 5084

South Asian (SAS) AF: 0.181 AC: 856 AN: 4732

European-Finnish (FIN) AF: 0.0959 AC: 960 AN: 10008

Middle Eastern (MID) AF: 0.0862 AC: 25 AN: 290

European-Non Finnish (NFE) AF: 0.118 AC: 7992 AN: 67750

Other (OTH) AF: 0.119 AC: 247 AN: 2082

Alfa AF: 0.0966 Hom.: 388

Bravo AF: 0.112

Asia WGS AF: 0.381 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17014226; hg19: chr2-34085608;