rs134220

Positions:

• chr22-35134490-T-C

Variant summary

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

The NR_126356.1(LINC01399):​n.513-14423A>G 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 0.118 in 152,224 control chromosomes in the GnomAD database, including 1,145 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 0.12 (1145 hom., cov: 32)
• Consequence: LINC01399 NR_126356.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01399	NR_126356.1	n.513-14423A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01399	ENST00000423311.1	n.513-14423A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17900 AN: 152106 Hom.: 1146 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.118 AC: 17905 AN: 152224 Hom.: 1145 Cov.: 32 AF XY: 0.118 AC XY: 8762 AN XY: 74420

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00753

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.107

Alfa AF: 0.130 Hom.: 1756

Bravo AF: 0.109

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs134220; hg19: chr22-35530483;