22-35164206-CAAAAA-CAAAAAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000423311.1(LINC01399):​n.512+7228_512+7229insT 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 0.34 (7968 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01399	NR_126356.1	n.512+7228dupT		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+7229insT		intron_variant	Intron 4 of 5	3
LINC01399	ENST00000798716.1	n.352+7228_352+7229insT		intron_variant	Intron 3 of 3
ENSG00000238153	ENST00000414048.1	n.-98_-97insA		upstream_gene_variant		6

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

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

African (AFR) AF: 0.547 AC: 16659 AN: 30480

American (AMR) AF: 0.295 AC: 3025 AN: 10264

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 711 AN: 3064

East Asian (EAS) AF: 0.603 AC: 2415 AN: 4006

South Asian (SAS) AF: 0.369 AC: 1171 AN: 3172

European-Finnish (FIN) AF: 0.244 AC: 955 AN: 3920

Middle Eastern (MID) AF: 0.298 AC: 71 AN: 238

European-Non Finnish (NFE) AF: 0.228 AC: 13327 AN: 58406

Other (OTH) AF: 0.329 AC: 498 AN: 1514

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;