dbSNP rs10483362: ENSG00000258558:n.209-9728G>A (chr14-30791724-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000554665.1(ENSG00000258558):n.209-9728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 152,122 control chromosomes in the GnomAD database, including 32 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 0.014 ( 32 hom., cov: 31)

Consequence

ENSG00000258558
ENST00000554665.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.550

Publications

1 publications found

Variant links:

Genes affected

ENSG00000258558 (HGNC:):

ENSG00000258558 links:

RPL12P5 (HGNC:19669): (ribosomal protein L12 pseudogene 5)

RPL12P5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 = 0.0666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258558	ENST00000554665.1 link	n.209-9728G>A		intron_variant	Intron 1 of 2	3
RPL12P5	ENST00000475149.1 link	n.*235C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.0136

AC:

2062

AN:

152002

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0133

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00989

Gnomad ASJ

AF:

0.00952

Gnomad EAS

AF:

0.0721

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.00925

Gnomad OTH

AF:

0.0235

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

GnomAD4 genome

AF:

0.0136

AC:

2065

AN:

152122

Hom.:

Cov.:

AF XY:

0.0145

AC XY:

1075

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0133

AC:

553

AN:

41492

American (AMR)

AF:

0.00988

AC:

151

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00952

AC:

AN:

3466

East Asian (EAS)

AF:

0.0726

AC:

375

AN:

5164

South Asian (SAS)

AF:

0.0547

AC:

263

AN:

4808

European-Finnish (FIN)

AF:

0.000189

AC:

AN:

10590

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00925

AC:

629

AN:

68000

Other (OTH)

AF:

0.0228

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

198

298

397

496

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0118

Hom.:

Bravo

AF:

0.0136

Asia WGS

AF:

0.0730

AC:

254

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

1.8

(source)

DANN

Benign

0.47

PhyloP100

0.55

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over