22-35164206-CAAAAA-CAAAAAAAA

Variant names:

• chr22-35164206-C-CAAA
• rs134315
• ENST00000423311.1:n.512+7228_512+7229insTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000423311.1(LINC01399):​n.512+7228_512+7229insTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0033 (10 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 3 publications found

Genes affected

LINC01399 (HGNC:):

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01399	NR_126356.1	n.512+7226_512+7228dupTTT		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000423311.1	n.512+7228_512+7229insTTT		intron_variant	Intron 4 of 5	3
LINC01399	ENST00000798716.1	n.352+7228_352+7229insTTT		intron_variant	Intron 3 of 3
ENSG00000238153	ENST00000414048.1	n.-98_-97insAAA		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.00333 AC: 386 AN: 115966 Hom.: 10 Cov.: 0

Gnomad AFR AF: 0.00774

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00380

Gnomad ASJ AF: 0.00196

Gnomad EAS AF: 0.00149

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.000510

Gnomad MID AF: 0.00391

Gnomad NFE AF: 0.00147

Gnomad OTH AF: 0.00397

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00334 AC: 387 AN: 115938 Hom.: 10 Cov.: 0 AF XY: 0.00336 AC XY: 180 AN XY: 53620

African (AFR) AF: 0.00773 AC: 236 AN: 30538

American (AMR) AF: 0.00390 AC: 40 AN: 10262

Ashkenazi Jewish (ASJ) AF: 0.00196 AC: 6 AN: 3062

East Asian (EAS) AF: 0.00150 AC: 6 AN: 4006

South Asian (SAS) AF: 0.00126 AC: 4 AN: 3174

European-Finnish (FIN) AF: 0.000510 AC: 2 AN: 3922

Middle Eastern (MID) AF: 0.00420 AC: 1 AN: 238

European-Non Finnish (NFE) AF: 0.00147 AC: 86 AN: 58396

Other (OTH) AF: 0.00396 AC: 6 AN: 1516

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs134315; hg19: chr22-35560199;