22-35164206-CAAAAA-CAAAAAAA

Position:

• chr22-35164206-CAAAAA-CAAAAAAA

Variant summary

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

The NR_126356.1(LINC01399):​n.512+7228_512+7229insTT variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 115,624 control chromosomes in the GnomAD database, including 20,533 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.54 (20533 hom., cov: 0)
  • Exomes 𝑓: 0.30 (0 hom.)
• 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 (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01399	NR_126356.1	n.512+7228_512+7229insTT		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+7229insTT		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.545 AC: 63045 AN: 115642 Hom.: 20547 Cov.: 0

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.591

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.572

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.545 AC: 63006 AN: 115614 Hom.: 20533 Cov.: 0 AF XY: 0.538 AC XY: 28797 AN XY: 53488

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.572

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;