rs713969

chr22-35203000-C-Achr22-35203000-C-G

Variant summary

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

The NR_126356.1(LINC01399):n.60-7981G>T 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 0.444 in 152,006 control chromosomes in the GnomAD database, including 18,913 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 0.44 (18913 hom., cov: 32)
• Consequence: LINC01399 NR_126356.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01399	NR_126356.1	n.60-7981G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01399	ENST00000423311.1	n.60-7981G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67390 AN: 151888 Hom.: 18864 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.444 AC: 67497 AN: 152006 Hom.: 18913 Cov.: 32 AF XY: 0.442 AC XY: 32825 AN XY: 74270

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.403

Alfa AF: 0.321 Hom.: 5311

Bravo AF: 0.460

Asia WGS AF: 0.508 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.23
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713969; hg19: chr22-35598993;