22-35164206-CAAAAA-CAAAAAAA

Variant names:

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

Variant summary

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

The ENST00000423311.1(LINC01399):​n.512+7228_512+7229insTT variant causes a intron 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 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 (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01399	NR_126356.1	n.512+7227_512+7228dupTT		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+7229insTT		intron_variant	Intron 4 of 5	3
LINC01399	ENST00000798716.1	n.352+7228_352+7229insTT		intron_variant	Intron 3 of 3
ENSG00000238153	ENST00000414048.1	n.-98_-97insAA		upstream_gene_variant		6

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

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: 0.375 AC: 3 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.183 AC: 5561 AN: 30436

American (AMR) AF: 0.627 AC: 6429 AN: 10252

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2166 AN: 3062

East Asian (EAS) AF: 0.388 AC: 1555 AN: 4004

South Asian (SAS) AF: 0.570 AC: 1804 AN: 3166

European-Finnish (FIN) AF: 0.657 AC: 2572 AN: 3914

Middle Eastern (MID) AF: 0.581 AC: 137 AN: 236

European-Non Finnish (NFE) AF: 0.710 AC: 41323 AN: 58216

Other (OTH) AF: 0.572 AC: 863 AN: 1510

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;