rs134378

Positions:

• chr22-35173697-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.223-1237A>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 0.553 in 152,162 control chromosomes in the GnomAD database, including 27,382 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 0.55 (27382 hom., cov: 34)
• Consequence: LINC01399 NR_126356.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01399	NR_126356.1	n.223-1237A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01399	ENST00000423311.1	n.223-1237A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84142 AN: 152046 Hom.: 27384 Cov.: 34

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.553 AC: 84143 AN: 152162 Hom.: 27382 Cov.: 34 AF XY: 0.555 AC XY: 41291 AN XY: 74394

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.595

Alfa AF: 0.692 Hom.: 49676

Bravo AF: 0.537

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs134378; hg19: chr22-35569690;