rs7397814

Positions:

• chr12-9394366-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02367	NR_120479.1	n.2363-165T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02367	ENST00000567749.1	n.2363-165T>C		intron_variant		1
LINC02367	ENST00000652814.1	n.453-165T>C		intron_variant
LINC02367	ENST00000656726.1	n.1214-1353T>C		intron_variant

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

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.871

Alfa AF: 0.829 Hom.: 24064

Bravo AF: 0.866

Asia WGS AF: 0.892 AC: 3100 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7397814; hg19: chr12-9546962;