rs710052

Variant names:

• chr14-61643957-C-G
• rs710052
• ENST00000556347.1:c.418-13648C>G

Your query was ambiguous. Multiple possible variants found:

• chr14-61643957-C-G
• chr14-61643957-C-T

Variant summary

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

The ENST00000556347.1(ENSG00000258989):​c.418-13648C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,972 control chromosomes in the GnomAD database, including 31,813 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 0.59 (31813 hom., cov: 30)
• Consequence: ENSG00000258989 ENST00000556347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

ENSG00000258989 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03033	NR_039985.1	n.222-7005C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258989	ENST00000556347.1	c.418-13648C>G		intron_variant	Intron 3 of 3	4		ENSP00000452401.1
LINC03033	ENST00000229465.10	n.222-7005C>G		intron_variant	Intron 1 of 4	2
LINC03033	ENST00000556569.5	n.357-7005C>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89007 AN: 151854 Hom.: 31801 Cov.: 30

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.586 AC: 89034 AN: 151972 Hom.: 31813 Cov.: 30 AF XY: 0.594 AC XY: 44111 AN XY: 74276

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.589

Alfa AF: 0.567 Hom.: 2179

Bravo AF: 0.552

Asia WGS AF: 0.639 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.2
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs710052; hg19: chr14-62110675;