5-164462274-G-T

Variant names:

• chr5-164462274-G-T
• rs6556756
• ENST00000486913.3:n.86-24395G>T

Variant summary

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

The ENST00000486913.3(LINC03000):​n.86-24395G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,174 control chromosomes in the GnomAD database, including 60,481 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 0.89 (60481 hom., cov: 32)
• Consequence: LINC03000 ENST00000486913.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

LINC03000 (HGNC:56116): (long intergenic non-protein coding RNA 3000)

LINC02143 (HGNC:53003): (long intergenic non-protein coding RNA 2143)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02143	NR_105064.1	n.120+2525C>A		intron_variant	Intron 2 of 3
LINC03000	XR_001742489.2	n.576+108050G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03000	ENST00000486913.3	n.86-24395G>T		intron_variant	Intron 1 of 2	2
LINC03000	ENST00000517508.5	n.586-24395G>T		intron_variant	Intron 2 of 5	4
LINC03000	ENST00000519329.2	n.316-24400G>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135081 AN: 152056 Hom.: 60420 Cov.: 32

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.888 AC: 135201 AN: 152174 Hom.: 60481 Cov.: 32 AF XY: 0.886 AC XY: 65942 AN XY: 74394

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.894

Alfa AF: 0.875 Hom.: 90302

Bravo AF: 0.891

Asia WGS AF: 0.750 AC: 2609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6556756; hg19: chr5-163889280;