5-79964396-C-T

Position:

• chr5-79964396-C-T

Variant summary

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

The ENST00000503167.1(LINC01455):​n.522-3191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,130 control chromosomes in the GnomAD database, including 35,406 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 0.68 (35406 hom., cov: 33)
• Consequence: LINC01455 ENST00000503167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

Genes affected

LINC01455 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01455	NR_131226.1	n.522-3191C>T		intron_variant
LOC105379048	XR_948500.3	n.199-11241C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01455	ENST00000503167.1	n.522-3191C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103250 AN: 152012 Hom.: 35361 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.679 AC: 103347 AN: 152130 Hom.: 35406 Cov.: 33 AF XY: 0.680 AC XY: 50569 AN XY: 74372

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.675

Alfa AF: 0.633 Hom.: 18470

Bravo AF: 0.682

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6453494; hg19: chr5-79260219;