rs9834177

Variant summary

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

The NM_024628.6(SLC12A8):​c.1922-1316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.20 ( 769 hom., cov: 10)

Consequence

SLC12A8
NM_024628.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.327
Variant links:
Genes affected
SLC12A8 (HGNC:15595): (solute carrier family 12 member 8) This gene is thought to be a candidate for psoriasis susceptibility. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Sep 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC12A8NM_024628.6 linkuse as main transcriptc.1922-1316G>A intron_variant ENST00000469902.6 NP_078904.4
SLC12A8NM_001195483.2 linkuse as main transcriptc.1922-1316G>A intron_variant NP_001182412.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC12A8ENST00000469902.6 linkuse as main transcriptc.1922-1316G>A intron_variant 2 NM_024628.6 ENSP00000418783 P1A0AV02-1

Frequencies

GnomAD3 genomes
AF:
0.197
AC:
11931
AN:
60522
Hom.:
767
Cov.:
10
show subpopulations
Gnomad AFR
AF:
0.299
Gnomad AMI
AF:
0.0893
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.455
Gnomad SAS
AF:
0.222
Gnomad FIN
AF:
0.0453
Gnomad MID
AF:
0.186
Gnomad NFE
AF:
0.139
Gnomad OTH
AF:
0.173
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.197
AC:
11936
AN:
60526
Hom.:
769
Cov.:
10
AF XY:
0.194
AC XY:
5515
AN XY:
28388
show subpopulations
Gnomad4 AFR
AF:
0.299
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.202
Gnomad4 EAS
AF:
0.456
Gnomad4 SAS
AF:
0.220
Gnomad4 FIN
AF:
0.0453
Gnomad4 NFE
AF:
0.139
Gnomad4 OTH
AF:
0.174
Alfa
AF:
0.101
Hom.:
82
Bravo
AF:
0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.48
DANN
Benign
0.64

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.

Other links and lift over

dbSNP: rs9834177; hg19: chr3-124808530; API