Variant 16-67943793-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005072.5(SLC12A4):c.*1047T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 697,360 control chromosomes in the GnomAD database, including 434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.037 ( 308 hom., cov: 33)

Exomes 𝑓: 0.0063 ( 126 hom. )

Consequence

SLC12A4
NM_005072.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.68

Variant links:

Genes affected

SLC12A4 (HGNC:10913): (solute carrier family 12 member 4) This gene encodes a member of the SLC12A transporter family. The encoded protein mediates the coupled movement of potassium and chloride ions across the plasma membrane. This gene is expressed ubiquitously. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jan 2013]

SLC12A4 links:

LCAT (HGNC:6522): (lecithin-cholesterol acyltransferase) This gene encodes the extracellular cholesterol esterifying enzyme, lecithin-cholesterol acyltransferase. The esterification of cholesterol is required for cholesterol transport. Mutations in this gene have been found to cause fish-eye disease as well as LCAT deficiency. [provided by RefSeq, Jul 2008]

LCAT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 16-67943793-A-C is Benign according to our data. Variant chr16-67943793-A-C is described in ClinVar as [Benign]. Clinvar id is 1282461.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-67943793-A-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A4	NM_005072.5 linkuse as main transcript	c.*1047T>G		3_prime_UTR_variant	24/24	ENST00000316341.8
LCAT	NM_000229.2 linkuse as main transcript	c.154+155T>G		intron_variant		ENST00000264005.10

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A4	ENST00000316341.8 linkuse as main transcript	c.*1047T>G	3_prime_UTR_variant	24/24	1	NM_005072.5	P1	Q9UP95-1
LCAT	ENST00000264005.10 linkuse as main transcript	c.154+155T>G	intron_variant		1	NM_000229.2	P1
LCAT	ENST00000575467.5 linkuse as main transcript	c.154+155T>G	intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0374

AC:

5687

AN:

152092

Hom.:

306

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0165

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00206

Gnomad OTH

AF:

0.0302

GnomAD4 exome

AF:

0.00630

AC:

3436

AN:

545150

Hom.:

126

Cov.:

AF XY:

0.00572

AC XY:

1599

AN XY:

279580

show subpopulations

Gnomad4 AFR exome

AF:

0.128

Gnomad4 AMR exome

AF:

0.0116

Gnomad4 ASJ exome

AF:

0.0119

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000808

Gnomad4 FIN exome

AF:

0.00269

Gnomad4 NFE exome

AF:

0.00206

Gnomad4 OTH exome

AF:

0.0122

GnomAD4 genome

AF:

0.0375

AC:

5701

AN:

152210

Hom.:

308

Cov.:

AF XY:

0.0361

AC XY:

2684

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.0165

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00206

Gnomad4 OTH

AF:

0.0294

Alfa

AF:

0.00962

Hom.:

Bravo

AF:

0.0420

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 04, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.10

DANN

Benign

0.37

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over