ENST00000423311.1:n.60-8770T>C

Variant names:

• chr22-35203789-A-G
• rs5999762
• ENST00000423311.1:n.60-8770T>C

Variant summary

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

The ENST00000423311.1(LINC01399):​n.60-8770T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,012 control chromosomes in the GnomAD database, including 16,149 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 0.38 (16149 hom., cov: 32)
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 3 publications found

Genes affected

LINC01399 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423311.1. 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
	LINC01399	NR_126356.1		n.60-8770T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01399	ENST00000423311.1	TSL:3	n.60-8770T>C		intron	N/A
	LINC01399	ENST00000798716.1		n.62+27209T>C		intron	N/A
	LINC01399	ENST00000798717.1		n.59-8770T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58283 AN: 151894 Hom.: 16101 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.384 AC: 58394 AN: 152012 Hom.: 16149 Cov.: 32 AF XY: 0.383 AC XY: 28439 AN XY: 74298

African (AFR) AF: 0.773 AC: 32050 AN: 41448

American (AMR) AF: 0.296 AC: 4524 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3094 AN: 5156

South Asian (SAS) AF: 0.316 AC: 1522 AN: 4812

European-Finnish (FIN) AF: 0.215 AC: 2275 AN: 10588

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13250 AN: 67948

Other (OTH) AF: 0.333 AC: 704 AN: 2114

Alfa AF: 0.363 Hom.: 2617

Bravo AF: 0.407

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.56
DANN	Benign	0.62
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs5999762; hg19: chr22-35599782;