dbSNP rs2255959: ENSG00000258989:c.418-35937G>A (chr14-61621668-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.275

Variant links:

Genes affected

ENSG00000258989 (HGNC:):

ENSG00000258989 links:

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

LINC03033 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 link	n.222-29294G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000258989	ENST00000556347.1 link	c.418-35937G>A	intron_variant	Intron 3 of 3	4	ENSP00000452401.1	H0YJX3
LINC03033	ENST00000229465.10 link	n.222-29294G>A	intron_variant	Intron 1 of 4	2
LINC03033	ENST00000556569.5 link	n.357-29294G>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.766

AC:

116421

AN:

151904

Hom.:

50145

Cov.:

show subpopulations

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.:

AF XY:

0.773

AC XY:

57467

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.334

Gnomad4 AMR

AF:

0.860

Gnomad4 ASJ

AF:

0.853

Gnomad4 EAS

AF:

0.974

Gnomad4 SAS

AF:

0.889

Gnomad4 FIN

AF:

0.978

Gnomad4 NFE

AF:

0.943

Gnomad4 OTH

AF:

0.780

Alfa

AF:

0.899

Hom.:

81626

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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over