Genetic Variant SLC12A8:n.1705A>G (chr3-125083387-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000465475.5(SLC12A8):n.1705A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 157,016 control chromosomes in the GnomAD database, including 30,100 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 0.61 ( 29387 hom., cov: 29)

Exomes 𝑓: 0.51 ( 713 hom. )

Consequence

SLC12A8
ENST00000465475.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

9 publications found

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]

SLC12A8 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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC12A8	NM_024628.6 link	c.*503A>G		3_prime_UTR_variant	Exon 14 of 14	ENST00000469902.6	NP_078904.4
SLC12A8	NM_001195483.2 link	c.*503A>G		3_prime_UTR_variant	Exon 13 of 13		NP_001182412.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC12A8	ENST00000469902.6 link	c.*503A>G		3_prime_UTR_variant	Exon 14 of 14	2	NM_024628.6	ENSP00000418783.1

Frequencies

GnomAD3 genomes

AF:

0.610

AC:

92591

AN:

151690

Hom.:

29336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.781

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.624

Gnomad ASJ

AF:

0.445

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.512

Gnomad FIN

AF:

0.616

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.524

Gnomad OTH

AF:

0.563

GnomAD4 exome

AF:

0.507

AC:

2635

AN:

5202

Hom.:

713

Cov.:

AF XY:

0.501

AC XY:

1378

AN XY:

2752

show subpopulations

African (AFR)

AF:

0.867

AC:

AN:

American (AMR)

AF:

0.569

AC:

691

AN:

1214

Ashkenazi Jewish (ASJ)

AF:

0.550

AC:

AN:

East Asian (EAS)

AF:

0.622

AC:

AN:

South Asian (SAS)

AF:

0.444

AC:

248

AN:

558

European-Finnish (FIN)

AF:

0.450

AC:

AN:

Middle Eastern (MID)

AF:

0.833

AC:

AN:

European-Non Finnish (NFE)

AF:

0.485

AC:

1476

AN:

3044

Other (OTH)

AF:

0.516

AC:

AN:

192

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

129

194

258

323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.611

AC:

92709

AN:

151814

Hom.:

29387

Cov.:

AF XY:

0.613

AC XY:

45518

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.781

AC:

32334

AN:

41398

American (AMR)

AF:

0.625

AC:

9538

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.445

AC:

1541

AN:

3460

East Asian (EAS)

AF:

0.589

AC:

3024

AN:

5138

South Asian (SAS)

AF:

0.512

AC:

2454

AN:

4796

European-Finnish (FIN)

AF:

0.616

AC:

6490

AN:

10540

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.524

AC:

35550

AN:

67906

Other (OTH)

AF:

0.561

AC:

1185

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1736

3472

5209

6945

8681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.544

Hom.:

80962

Bravo

AF:

0.618

Asia WGS

AF:

0.544

AC:

1892

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.3

(source)

DANN

Benign

0.85

PhyloP100

0.31

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over