chr2-34496492-C-T

Variant names:

• chr2-34496492-C-T
• rs7583665
• ENST00000422558.1:n.475+111923C>T

Variant summary

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

The ENST00000422558.1(LINC01320):​n.475+111923C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 132,840 control chromosomes in the GnomAD database, including 1,487 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 0.068 (1487 hom., cov: 23)
• Consequence: LINC01320 ENST00000422558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422558.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000422558.1	TSL:4	n.475+111923C>T		intron	N/A
	LINC01320	ENST00000650021.1		n.219+111923C>T		intron	N/A
	LINC01320	ENST00000654103.1		n.597+19863C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 9009 AN: 132718 Hom.: 1477 Cov.: 23

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00417

Gnomad MID AF: 0.0630

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0681 AC: 9048 AN: 132840 Hom.: 1487 Cov.: 23 AF XY: 0.0662 AC XY: 4273 AN XY: 64544

African (AFR) AF: 0.176 AC: 7062 AN: 40226

American (AMR) AF: 0.0420 AC: 531 AN: 12632

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 73 AN: 3012

East Asian (EAS) AF: 0.00 AC: 0 AN: 5140

South Asian (SAS) AF: 0.0288 AC: 124 AN: 4302

European-Finnish (FIN) AF: 0.00417 AC: 34 AN: 8152

Middle Eastern (MID) AF: 0.0595 AC: 15 AN: 252

European-Non Finnish (NFE) AF: 0.0194 AC: 1100 AN: 56822

Other (OTH) AF: 0.0621 AC: 109 AN: 1756

Alfa AF: 0.0306 Hom.: 147

Asia WGS AF: 0.0280 AC: 95 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.25
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7583665; hg19: chr2-34721559;