22-35164206-CAAAAA-CAAAAAA

Position:

• chr22-35164206-CAAAAA-CAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_126356.1(LINC01399):​n.512+7228_512+7229insT variant causes a intron, non coding transcript 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 0.34 (7968 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01399 NR_126356.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01399	NR_126356.1	n.512+7228_512+7229insT		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01399	ENST00000423311.1	n.512+7228_512+7229insT		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 38981 AN: 115914 Hom.: 7959 Cov.: 0

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.328

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

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.336 AC: 38982 AN: 115888 Hom.: 7968 Cov.: 0 AF XY: 0.341 AC XY: 18297 AN XY: 53598

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs134315; hg19: chr22-35560199;