Variant 7-100826964-CG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001363494.1(SLC12A9):c.-64delG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,423,328 control chromosomes in the GnomAD database, including 35,102 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 4391 hom., cov: 21)

Exomes 𝑓: 0.26 ( 30711 hom. )

Consequence

SLC12A9
NM_001363494.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.17

Variant links:

Genes affected

EPHB4 (HGNC:3395): (EPH receptor B4) Ephrin receptors and their ligands, the ephrins, mediate numerous developmental processes, particularly in the nervous system. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. The Eph family of receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Ephrin receptors make up the largest subgroup of the receptor tyrosine kinase (RTK) family. The protein encoded by this gene binds to ephrin-B2 and plays an essential role in vascular development. [provided by RefSeq, Jul 2008]

EPHB4 links:

EPHB4 (HGNC:):

EPHB4 links:

SLC12A9 (HGNC:17435): (solute carrier family 12 member 9) Predicted to enable potassium:chloride symporter activity. Predicted to be involved in cell volume homeostasis; inorganic ion homeostasis; and inorganic ion transmembrane transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

SLC12A9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 7-100826964-CG-C is Benign according to our data. Variant chr7-100826964-CG-C is described in ClinVar as [Benign]. Clinvar id is 811642.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-100826964-CG-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHB4	NM_004444.5 linkuse as main transcript	c.52+14delC		intron_variant		ENST00000358173.8	NP_004435.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHB4	ENST00000358173.8 linkuse as main transcript	c.52+14delC		intron_variant		1	NM_004444.5	ENSP00000350896.3		P54760-1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

34674

AN:

140010

Hom.:

4395

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.00334

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.412

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.268

GnomAD3 exomes

AF:

0.236

AC:

35645

AN:

150902

Hom.:

2771

AF XY:

0.244

AC XY:

19787

AN XY:

81178

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.146

Gnomad ASJ exome

AF:

0.328

Gnomad EAS exome

AF:

0.00734

Gnomad SAS exome

AF:

0.251

Gnomad FIN exome

AF:

0.298

Gnomad NFE exome

AF:

0.286

Gnomad OTH exome

AF:

0.261

GnomAD4 exome

AF:

0.264

AC:

338809

AN:

1283222

Hom.:

30711

Cov.:

AF XY:

0.265

AC XY:

168192

AN XY:

633616

show subpopulations

Gnomad4 AFR exome

AF:

0.191

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.332

Gnomad4 EAS exome

AF:

0.00332

Gnomad4 SAS exome

AF:

0.263

Gnomad4 FIN exome

AF:

0.309

Gnomad4 NFE exome

AF:

0.274

Gnomad4 OTH exome

AF:

0.254

GnomAD4 genome

AF:

0.247

AC:

34668

AN:

140106

Hom.:

4391

Cov.:

AF XY:

0.247

AC XY:

16907

AN XY:

68490

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.345

Gnomad4 EAS

AF:

0.00335

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.319

Gnomad4 NFE

AF:

0.291

Gnomad4 OTH

AF:

0.265

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 29, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 12, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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