rs710059

Variant names:

• chr14-61639547-C-T
• rs710059
• ENST00000556347.1:c.418-18058C>T

Variant summary

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

The ENST00000556347.1(ENSG00000258989):​c.418-18058C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,054 control chromosomes in the GnomAD database, including 33,410 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 0.60 (33410 hom., cov: 32)
• Consequence: ENSG00000258989 ENST00000556347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 3 publications found

Genes affected

ENSG00000258989 (HGNC:):

LINC03033 (HGNC:44292): (long intergenic non-protein coding RNA 3033)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556347.1. 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
	LINC03033	NR_039985.1		n.222-11415C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258989	ENST00000556347.1	TSL:4	c.418-18058C>T		intron	N/A	ENSP00000452401.1	H0YJX3
	LINC03033	ENST00000229465.10	TSL:2	n.222-11415C>T		intron	N/A
	LINC03033	ENST00000556569.5	TSL:2	n.357-11415C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91945 AN: 151936 Hom.: 33404 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.605 AC: 91966 AN: 152054 Hom.: 33410 Cov.: 32 AF XY: 0.615 AC XY: 45755 AN XY: 74348

African (AFR) AF: 0.177 AC: 7349 AN: 41446

American (AMR) AF: 0.715 AC: 10927 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2350 AN: 3466

East Asian (EAS) AF: 0.752 AC: 3884 AN: 5168

South Asian (SAS) AF: 0.736 AC: 3554 AN: 4826

European-Finnish (FIN) AF: 0.889 AC: 9409 AN: 10582

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52369 AN: 67964

Other (OTH) AF: 0.614 AC: 1295 AN: 2110

Alfa AF: 0.681 Hom.: 4854

Bravo AF: 0.571

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.77
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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: rs710059;

hg19: chr14-62106265;