15-34230356-G-A

Position:

• chr15-34230356-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001365088.1(SLC12A6):​c.*3525C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,902 control chromosomes in the GnomAD database, including 1,136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1132 hom., cov: 32)
  • Exomes 𝑓: 0.098 (4 hom.)
• Consequence: SLC12A6 NM_001365088.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.60

Genes affected

SLC12A6 (HGNC:10914): (solute carrier family 12 member 6) This gene is a member of the K-Cl cotransporter (KCC) family. K-Cl cotransporters are integral membrane proteins that lower intracellular chloride concentrations below the electrochemical equilibrium potential. The proteins encoded by this gene are activated by cell swelling induced by hypotonic conditions. Alternate splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are associated with agenesis of the corpus callosum with peripheral neuropathy. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 15-34230356-G-A is Benign according to our data. Variant chr15-34230356-G-A is described in ClinVar as [Benign]. Clinvar id is 315547.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC12A6	NM_001365088.1	c.*3525C>T		3_prime_UTR_variant	26/26	ENST00000354181.8	NP_001352017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC12A6	ENST00000354181.8	c.*3525C>T		3_prime_UTR_variant	26/26	1	NM_001365088.1	ENSP00000346112	A1
SLC12A6	ENST00000290209.9	c.*3525C>T		3_prime_UTR_variant	25/25	1		ENSP00000290209	P3
SLC12A6	ENST00000676379.1	c.*2144C>T		3_prime_UTR_variant	26/26			ENSP00000502539

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17689 AN: 152032 Hom.: 1135 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.135

GnomAD4 exome AF: 0.0984 AC: 74 AN: 752 Hom.: 4 Cov.: 0 AF XY: 0.0988 AC XY: 51 AN XY: 516

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.200

Gnomad4 FIN exome AF: 0.136

Gnomad4 NFE exome AF: 0.0798

Gnomad4 OTH exome AF: 0.0500

GnomAD4 genome AF: 0.116 AC: 17692 AN: 152150 Hom.: 1132 Cov.: 32 AF XY: 0.118 AC XY: 8759 AN XY: 74372

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0642

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.135

Alfa AF: 0.111 Hom.: 957

Bravo AF: 0.122

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Agenesis of the corpus callosum with peripheral neuropathy Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs1133154; hg19: chr15-34522557;