2-34013902-C-T

Variant names:

• chr2-34013902-C-T
• rs2162008
• ENST00000366209.6:n.389+69349C>T

Variant summary

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

The ENST00000366209.6(LINC01320):​n.389+69349C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,146 control chromosomes in the GnomAD database, including 52,662 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 0.83 (52662 hom., cov: 32)
• Consequence: LINC01320 ENST00000366209.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366209.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01317	NR_126403.1		n.389+69349C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000366209.6	TSL:5	n.389+69349C>T		intron	N/A
	LINC01320	ENST00000442026.1	TSL:3	n.471-46848C>T		intron	N/A
	LINC01320	ENST00000771863.1		n.266-47117C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126341 AN: 152028 Hom.: 52622 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.831 AC: 126430 AN: 152146 Hom.: 52662 Cov.: 32 AF XY: 0.835 AC XY: 62131 AN XY: 74392

African (AFR) AF: 0.790 AC: 32769 AN: 41478

American (AMR) AF: 0.875 AC: 13372 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2811 AN: 3470

East Asian (EAS) AF: 0.806 AC: 4176 AN: 5178

South Asian (SAS) AF: 0.827 AC: 3990 AN: 4822

European-Finnish (FIN) AF: 0.889 AC: 9420 AN: 10592

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.840 AC: 57141 AN: 68010

Other (OTH) AF: 0.812 AC: 1718 AN: 2116

Alfa AF: 0.841 Hom.: 8480

Bravo AF: 0.828

Asia WGS AF: 0.775 AC: 2695 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.74
DANN	Benign	0.32
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2162008; hg19: chr2-34238969;