rs12594698

Variant summary

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

The NM_000338.3(SLC12A1):​c.2486-2347C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,970 control chromosomes in the GnomAD database, including 6,727 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 0.28 ( 6727 hom., cov: 32)

Consequence

SLC12A1
NM_000338.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122
Variant links:
Genes affected
SLC12A1 (HGNC:10910): (solute carrier family 12 member 1) This gene encodes a kidney-specific sodium-potassium-chloride cotransporter that is expressed on the luminal membrane of renal epithelial cells of the thick ascending limb of Henle's loop and the macula densa. It plays a key role in concentrating urine and accounts for most of the NaCl resorption. It is sensitive to such diuretics as furosemide and bumetanide. Some Bartter-like syndromes result from defects in this gene. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their biological validity in humans has not been experimentally proven.[provided by RefSeq, May 2010]

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=-0.7).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC12A1NM_000338.3 linkuse as main transcriptc.2486-2347C>T intron_variant ENST00000380993.8 NP_000329.2
SLC12A1NM_001184832.2 linkuse as main transcriptc.2486-2347C>T intron_variant NP_001171761.1
SLC12A1NM_001384136.1 linkuse as main transcriptc.2486-2347C>T intron_variant NP_001371065.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC12A1ENST00000380993.8 linkuse as main transcriptc.2486-2347C>T intron_variant 5 NM_000338.3 ENSP00000370381 A1Q13621-1

Frequencies

GnomAD3 genomes
AF:
0.275
AC:
41712
AN:
151852
Hom.:
6699
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.434
Gnomad AMI
AF:
0.0614
Gnomad AMR
AF:
0.269
Gnomad ASJ
AF:
0.219
Gnomad EAS
AF:
0.412
Gnomad SAS
AF:
0.237
Gnomad FIN
AF:
0.208
Gnomad MID
AF:
0.174
Gnomad NFE
AF:
0.188
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.275
AC:
41794
AN:
151970
Hom.:
6727
Cov.:
32
AF XY:
0.274
AC XY:
20353
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.434
Gnomad4 AMR
AF:
0.270
Gnomad4 ASJ
AF:
0.219
Gnomad4 EAS
AF:
0.412
Gnomad4 SAS
AF:
0.237
Gnomad4 FIN
AF:
0.208
Gnomad4 NFE
AF:
0.188
Gnomad4 OTH
AF:
0.276
Alfa
AF:
0.212
Hom.:
1580
Bravo
AF:
0.286
Asia WGS
AF:
0.370
AC:
1287
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
CADD
Benign
2.0
DANN
Benign
0.63

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: rs12594698; hg19: chr15-48574956; API