rs2255959

Variant names:

• chr14-61621668-G-A
• rs2255959
• ENST00000556347.1:c.418-35937G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-61621668-G-A
• chr14-61621668-G-C

Variant summary

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

The ENST00000556347.1(ENSG00000258989):​c.418-35937G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,022 control chromosomes in the GnomAD database, including 50,150 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 0.77 (50150 hom., cov: 30)
• Consequence: ENSG00000258989 ENST00000556347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03033	NR_039985.1	n.222-29294G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258989	ENST00000556347.1	c.418-35937G>A		intron_variant	Intron 3 of 3	4		ENSP00000452401.1
LINC03033	ENST00000229465.10	n.222-29294G>A		intron_variant	Intron 1 of 4	2
LINC03033	ENST00000556569.5	n.357-29294G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116421 AN: 151904 Hom.: 50145 Cov.: 30

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.766 AC: 116449 AN: 152022 Hom.: 50150 Cov.: 30 AF XY: 0.773 AC XY: 57467 AN XY: 74346

African (AFR) AF: 0.334 AC: 13785 AN: 41332

American (AMR) AF: 0.860 AC: 13151 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2959 AN: 3468

East Asian (EAS) AF: 0.974 AC: 5041 AN: 5176

South Asian (SAS) AF: 0.889 AC: 4294 AN: 4828

European-Finnish (FIN) AF: 0.978 AC: 10369 AN: 10604

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.943 AC: 64104 AN: 68006

Other (OTH) AF: 0.780 AC: 1648 AN: 2112

Alfa AF: 0.880 Hom.: 100440

Bravo AF: 0.738

Asia WGS AF: 0.887 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		0.28
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

Other links and lift over

dbSNP: rs2255959; hg19: chr14-62088386;