Variant chr7-100826955-G-GC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001363494.1(SLC12A9):c.-65dupC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,433,544 control chromosomes in the GnomAD database, including 5,461 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.21 ( 3228 hom., cov: 22)

Exomes 𝑓: 0.17 ( 2233 hom. )

Consequence

SLC12A9
NM_001363494.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00400

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 -10 ACMG points.

BP6

Variant 7-100826955-G-GC is Benign according to our data. Variant chr7-100826955-G-GC is described in ClinVar as [Benign]. Clinvar id is 1276912.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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+23dupG		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+23dupG		intron_variant		1	NM_004444.5	ENSP00000350896.3		P54760-1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

27669

AN:

132926

Hom.:

3226

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.293

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.242

GnomAD3 exomes

AF:

0.211

AC:

25386

AN:

120156

Hom.:

309

AF XY:

0.203

AC XY:

13118

AN XY:

64638

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.349

Gnomad ASJ exome

AF:

0.0979

Gnomad EAS exome

AF:

0.398

Gnomad SAS exome

AF:

0.186

Gnomad FIN exome

AF:

0.117

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.215

GnomAD4 exome

AF:

0.168

AC:

218157

AN:

1300530

Hom.:

2233

Cov.:

AF XY:

0.167

AC XY:

107382

AN XY:

642252

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.313

Gnomad4 ASJ exome

AF:

0.0849

Gnomad4 EAS exome

AF:

0.406

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.161

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.208

AC:

27670

AN:

133014

Hom.:

3228

Cov.:

AF XY:

0.213

AC XY:

13732

AN XY:

64586

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.377

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.496

Gnomad4 SAS

AF:

0.235

Gnomad4 FIN

AF:

0.132

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.241

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 14, 2021

- -

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