5-165063080-C-T

Variant names:

• chr5-165063080-C-T
• rs2112172
• ENST00000519267.1:n.117+55668C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519267.1(LINC03000):​n.117+55668C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 150,474 control chromosomes in the GnomAD database, including 7,118 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 0.29 (7118 hom., cov: 29)
• Consequence: LINC03000 ENST00000519267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519267.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03000	ENST00000519267.1	TSL:3	n.117+55668C>T		intron	N/A
	LINC03000	ENST00000519570.5	TSL:3	n.451+55668C>T		intron	N/A
	LINC03000	ENST00000522303.5	TSL:5	n.290+55668C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 43996 AN: 150370 Hom.: 7099 Cov.: 29

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.293 AC: 44042 AN: 150474 Hom.: 7118 Cov.: 29 AF XY: 0.306 AC XY: 22449 AN XY: 73426

African (AFR) AF: 0.235 AC: 9623 AN: 41026

American (AMR) AF: 0.387 AC: 5855 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3462

East Asian (EAS) AF: 0.655 AC: 3350 AN: 5114

South Asian (SAS) AF: 0.357 AC: 1706 AN: 4780

European-Finnish (FIN) AF: 0.409 AC: 4106 AN: 10048

Middle Eastern (MID) AF: 0.241 AC: 70 AN: 290

European-Non Finnish (NFE) AF: 0.262 AC: 17748 AN: 67630

Other (OTH) AF: 0.301 AC: 632 AN: 2100

Alfa AF: 0.267 Hom.: 2840

Bravo AF: 0.290

Asia WGS AF: 0.466 AC: 1615 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.61
PhyloP100		-0.014

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2112172;

hg19: chr5-164490086;