dbSNP rs13975: 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	A0AV02-1
SLC12A8	NM_001195483.2 link	c.*503A>G		3_prime_UTR_variant	Exon 13 of 13		NP_001182412.2	A0AV02-1

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		A0AV02-1

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

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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