22-35130800-T-G

Position:

• chr22-35130800-T-G

Variant summary

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

The NR_126356.1(LINC01399):​n.513-10733A>C 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 0.558 in 151,986 control chromosomes in the GnomAD database, including 24,458 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 0.56 (24458 hom., cov: 31)
• Consequence: LINC01399 NR_126356.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01399	NR_126356.1	n.513-10733A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01399	ENST00000423311.1	n.513-10733A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84770 AN: 151868 Hom.: 24434 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.533

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.558 AC: 84838 AN: 151986 Hom.: 24458 Cov.: 31 AF XY: 0.548 AC XY: 40743 AN XY: 74296

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.528

Alfa AF: 0.540 Hom.: 43185

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs134215; hg19: chr22-35526793;