5-164462274-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486913.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02143	NR_105064.1		n.120+2525C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03000	ENST00000486913.3	TSL:2	n.86-24395G>T		intron	N/A
	LINC03000	ENST00000517508.5	TSL:4	n.586-24395G>T		intron	N/A
	LINC03000	ENST00000519329.3	TSL:3	n.933-24400G>T		intron	N/A

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

African (AFR) AF: 0.941 AC: 39082 AN: 41544

American (AMR) AF: 0.909 AC: 13887 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3067 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2847 AN: 5156

South Asian (SAS) AF: 0.865 AC: 4174 AN: 4824

European-Finnish (FIN) AF: 0.847 AC: 8975 AN: 10592

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60178 AN: 68004

Other (OTH) AF: 0.894 AC: 1883 AN: 2106

Alfa AF: 0.876 Hom.: 197949

Bravo AF: 0.891

Asia WGS AF: 0.750 AC: 2609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.29
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs6556756; hg19: chr5-163889280;