rs3752596

Positions:

• chr22-35194713-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000458450.1(LINC01399):​n.230C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 519,946 control chromosomes in the GnomAD database, including 141,895 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.62 (33720 hom., cov: 29)
  • Exomes 𝑓: 0.75 (108175 hom.)
• Consequence: LINC01399 ENST00000458450.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01399	NR_126356.1	n.222+144C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01399	ENST00000458450.1	n.230C>T		non_coding_transcript_exon_variant	1/1
LINC01399	ENST00000423311.1	n.222+144C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93410 AN: 151662 Hom.: 33726 Cov.: 29

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.668

GnomAD4 exome AF: 0.752 AC: 276985 AN: 368166 Hom.: 108175 Cov.: 2 AF XY: 0.758 AC XY: 149262 AN XY: 196894

Gnomad4 AFR exome AF: 0.224

Gnomad4 AMR exome AF: 0.745

Gnomad4 ASJ exome AF: 0.805

Gnomad4 EAS exome AF: 0.389

Gnomad4 SAS exome AF: 0.735

Gnomad4 FIN exome AF: 0.783

Gnomad4 NFE exome AF: 0.818

Gnomad4 OTH exome AF: 0.730

GnomAD4 genome AF: 0.615 AC: 93415 AN: 151780 Hom.: 33720 Cov.: 29 AF XY: 0.617 AC XY: 45751 AN XY: 74176

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.665

Alfa AF: 0.684 Hom.: 5661

Bravo AF: 0.592

Asia WGS AF: 0.533 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3752596; hg19: chr22-35590706;