5-79963521-T-C

Variant summary

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

The NR_131226.1(LINC01455):n.522-4066T>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 0.631 in 152,104 control chromosomes in the GnomAD database, including 30,448 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 0.63 (30448 hom., cov: 33)
• Consequence: LINC01455 NR_131226.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

Genes affected

LINC01455 (HGNC:50545): (long intergenic non-protein coding RNA 1455)

LOC105379048 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01455	NR_131226.1	n.522-4066T>C		intron_variant, non_coding_transcript_variant
LOC105379048	XR_948500.3	n.199-12116T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01455	ENST00000503167.1	n.522-4066T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95888 AN: 151986 Hom.: 30406 Cov.: 33

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.631 AC: 95987 AN: 152104 Hom.: 30448 Cov.: 33 AF XY: 0.630 AC XY: 46880 AN XY: 74354

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.616

Alfa AF: 0.628 Hom.: 3718

Bravo AF: 0.629

Asia WGS AF: 0.654 AC: 2276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.5
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: rs2471109; hg19: chr5-79259344;