chr15-48207506-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000338.3(SLC12A1):​c.-186-28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 395,452 control chromosomes in the GnomAD database, including 3,140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.075 ( 1211 hom., cov: 32)
Exomes 𝑓: 0.047 ( 1929 hom. )

Consequence

SLC12A1
NM_000338.3 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0450
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 15-48207506-C-T is Benign according to our data. Variant chr15-48207506-C-T is described in ClinVar as [Benign]. Clinvar id is 1276462.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC12A1NM_000338.3 linkuse as main transcriptc.-186-28C>T intron_variant ENST00000380993.8 NP_000329.2
SLC12A1NM_001184832.2 linkuse as main transcriptc.-186-28C>T intron_variant NP_001171761.1
SLC12A1NM_001384136.1 linkuse as main transcriptc.-186-28C>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.-186-28C>T intron_variant 5 NM_000338.3 ENSP00000370381 A1Q13621-1

Frequencies

GnomAD3 genomes
AF:
0.0747
AC:
11357
AN:
152052
Hom.:
1204
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.185
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0507
Gnomad ASJ
AF:
0.000289
Gnomad EAS
AF:
0.408
Gnomad SAS
AF:
0.115
Gnomad FIN
AF:
0.00236
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00141
Gnomad OTH
AF:
0.0689
GnomAD4 exome
AF:
0.0466
AC:
11335
AN:
243282
Hom.:
1929
Cov.:
3
AF XY:
0.0452
AC XY:
5577
AN XY:
123432
show subpopulations
Gnomad4 AFR exome
AF:
0.172
Gnomad4 AMR exome
AF:
0.0482
Gnomad4 ASJ exome
AF:
0.000232
Gnomad4 EAS exome
AF:
0.403
Gnomad4 SAS exome
AF:
0.0808
Gnomad4 FIN exome
AF:
0.00227
Gnomad4 NFE exome
AF:
0.00169
Gnomad4 OTH exome
AF:
0.0490
GnomAD4 genome
AF:
0.0748
AC:
11377
AN:
152170
Hom.:
1211
Cov.:
32
AF XY:
0.0771
AC XY:
5737
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.185
Gnomad4 AMR
AF:
0.0507
Gnomad4 ASJ
AF:
0.000289
Gnomad4 EAS
AF:
0.407
Gnomad4 SAS
AF:
0.114
Gnomad4 FIN
AF:
0.00236
Gnomad4 NFE
AF:
0.00141
Gnomad4 OTH
AF:
0.0777
Alfa
AF:
0.00119
Hom.:
0
Bravo
AF:
0.0829
Asia WGS
AF:
0.311
AC:
1077
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJan 26, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
CADD
Benign
5.1
DANN
Benign
0.70

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: rs16960656; hg19: chr15-48499703; API