chr2-33909672-C-G

Variant names:

• chr2-33909672-C-G
• rs1718711
• ENST00000366209.6:n.135-17168C>G

Variant summary

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

The ENST00000442026.1(LINC01320):​n.216-17168C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,038 control chromosomes in the GnomAD database, including 41,522 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 0.70 (41522 hom., cov: 32)
• Consequence: LINC01320 ENST00000442026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.135-17168C>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.135-17168C>G		intron_variant	Intron 2 of 5	5
LINC01320	ENST00000442026.1	n.216-17168C>G		intron_variant	Intron 3 of 6	3
LINC01320	ENST00000661209.1	n.314-17168C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106891 AN: 151920 Hom.: 41512 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.703 AC: 106925 AN: 152038 Hom.: 41522 Cov.: 32 AF XY: 0.703 AC XY: 52282 AN XY: 74324

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.741

Alfa AF: 0.771 Hom.: 5988

Bravo AF: 0.683

Asia WGS AF: 0.746 AC: 2595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1718711; hg19: chr2-34134739;