ENST00000458450.1:n.230C>T

Variant names:

• chr22-35194713-G-A
• rs3752596
• ENST00000458450.1:n.230C>T

Variant summary

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

The ENST00000458450.1(LINC01399):​n.230C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 519,946 control chromosomes in the GnomAD database, including 141,895 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 0.62 (33720 hom., cov: 29)
  • Exomes 𝑓: 0.75 (108175 hom.)
• Consequence: LINC01399 ENST00000458450.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500
• Publications: 7 publications found

Genes affected

LINC01399 (HGNC:50680): (long intergenic non-protein coding RNA 1399)

LINC01399 (HGNC:):

COX7BP1 (HGNC:16529): (COX7B pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COX7BP1		n.35194713G>A		intragenic_variant
LINC01399	NR_126356.1	n.222+144C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000458450.1	n.230C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01399	ENST00000798718.1	n.374C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01399	ENST00000798719.1	n.472C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93410 AN: 151662 Hom.: 33726 Cov.: 29

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.668

GnomAD4 exome AF: 0.752 AC: 276985 AN: 368166 Hom.: 108175 Cov.: 2 AF XY: 0.758 AC XY: 149262 AN XY: 196894

African (AFR) AF: 0.224 AC: 2311 AN: 10312

American (AMR) AF: 0.745 AC: 14284 AN: 19174

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 9281 AN: 11532

East Asian (EAS) AF: 0.389 AC: 10529 AN: 27088

South Asian (SAS) AF: 0.735 AC: 17055 AN: 23202

European-Finnish (FIN) AF: 0.783 AC: 21698 AN: 27722

Middle Eastern (MID) AF: 0.723 AC: 1173 AN: 1622

European-Non Finnish (NFE) AF: 0.818 AC: 184843 AN: 225852

Other (OTH) AF: 0.730 AC: 15811 AN: 21662

GnomAD4 genome AF: 0.615 AC: 93415 AN: 151780 Hom.: 33720 Cov.: 29 AF XY: 0.617 AC XY: 45751 AN XY: 74176

African (AFR) AF: 0.224 AC: 9274 AN: 41336

American (AMR) AF: 0.704 AC: 10732 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2753 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2057 AN: 5150

South Asian (SAS) AF: 0.682 AC: 3278 AN: 4808

European-Finnish (FIN) AF: 0.785 AC: 8288 AN: 10556

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.805 AC: 54685 AN: 67904

Other (OTH) AF: 0.665 AC: 1402 AN: 2108

Alfa AF: 0.668 Hom.: 5679

Bravo AF: 0.592

Asia WGS AF: 0.533 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs3752596; hg19: chr22-35590706;