rs7397814

Variant names:

• chr12-9394366-T-C
• rs7397814
• ENST00000567749.1:n.2363-165T>C

Variant summary

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

The ENST00000567749.1(LINC02367):​n.2363-165T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 151,796 control chromosomes in the GnomAD database, including 56,366 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 0.86 (56366 hom., cov: 29)
• Consequence: LINC02367 ENST00000567749.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 7 publications found

Genes affected

LINC02367 (HGNC:53290): (long intergenic non-protein coding RNA 2367)

ENSG00000308602 (HGNC:58687):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567749.1. 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
	LINC02367	NR_120479.1		n.2363-165T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02367	ENST00000567749.1	TSL:1	n.2363-165T>C		intron	N/A
	LINC02367	ENST00000652814.1		n.453-165T>C		intron	N/A
	LINC02367	ENST00000656726.1		n.1214-1353T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130370 AN: 151678 Hom.: 56306 Cov.: 29

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.860 AC: 130489 AN: 151796 Hom.: 56366 Cov.: 29 AF XY: 0.859 AC XY: 63770 AN XY: 74200

African (AFR) AF: 0.943 AC: 38975 AN: 41326

American (AMR) AF: 0.841 AC: 12823 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2960 AN: 3470

East Asian (EAS) AF: 0.938 AC: 4853 AN: 5174

South Asian (SAS) AF: 0.873 AC: 4191 AN: 4798

European-Finnish (FIN) AF: 0.823 AC: 8646 AN: 10500

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55237 AN: 67970

Other (OTH) AF: 0.871 AC: 1829 AN: 2100

Alfa AF: 0.848 Hom.: 42929

Bravo AF: 0.866

Asia WGS AF: 0.892 AC: 3100 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.94

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7397814;

hg19: chr12-9546962;