22-35130800-T-G

Variant names:

• chr22-35130800-T-G
• rs134215
• ENST00000423311.1:n.513-10733A>C

Variant summary

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

The ENST00000423311.1(LINC01399):​n.513-10733A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,986 control chromosomes in the GnomAD database, including 24,458 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 0.56 (24458 hom., cov: 31)
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01399	NR_126356.1		n.513-10733A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01399	ENST00000423311.1	TSL:3	n.513-10733A>C		intron	N/A
	LINC01399	ENST00000798716.1		n.352+40635A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84770 AN: 151868 Hom.: 24434 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.558 AC: 84838 AN: 151986 Hom.: 24458 Cov.: 31 AF XY: 0.548 AC XY: 40743 AN XY: 74296

African (AFR) AF: 0.656 AC: 27172 AN: 41412

American (AMR) AF: 0.504 AC: 7708 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3468

East Asian (EAS) AF: 0.174 AC: 899 AN: 5178

South Asian (SAS) AF: 0.432 AC: 2081 AN: 4816

European-Finnish (FIN) AF: 0.518 AC: 5471 AN: 10562

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38070 AN: 67952

Other (OTH) AF: 0.528 AC: 1116 AN: 2114

Alfa AF: 0.549 Hom.: 69884

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs134215; hg19: chr22-35526793;