Genetic Variant SLC9A7:c.*7259C>A (chrX-46599693-G-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001257291.2(SLC9A7):c.*7259C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.55 ( 12013 hom., 17717 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

SLC9A7
NM_001257291.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610

Publications

3 publications found

Variant links:

Genes affected

SLC9A7 (HGNC:17123): (solute carrier family 9 member A7) This gene encodes a sodium and potassium/ proton antiporter that is a member of the solute carrier family 9 protein family. The encoded protein is primarily localized to the trans-Golgi network and is involved in maintaining pH homeostasis in organelles along the secretory and endocytic pathways. This protein may enhance cell growth of certain breast tumors. This gene is part of a gene cluster on chromosome Xp11.23. A pseudogene of this gene is found on chromosome 12. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

SLC9A7 Gene-Disease associations (from GenCC):

intellectual developmental disorder, X-linked 108
Inheritance: XL, Unknown Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, PanelApp Australia
non-syndromic X-linked intellectual disability
Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

SLC9A7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001257291.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9A7	NM_001257291.2	MANE Select	c.*7259C>A		3_prime_UTR	Exon 17 of 17	NP_001244220.1	A0A087WXD1
	SLC9A7	NM_032591.3		c.*7259C>A		3_prime_UTR	Exon 17 of 17	NP_115980.1	Q96T83

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9A7	ENST00000616978.5	TSL:1 MANE Select	c.*7259C>A		3_prime_UTR	Exon 17 of 17	ENSP00000480916.1	A0A087WXD1

Frequencies

GnomAD3 genomes

AF:

0.551

AC:

60450

AN:

109786

Hom.:

12015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.623

Gnomad AMI

AF:

0.568

Gnomad AMR

AF:

0.554

Gnomad ASJ

AF:

0.574

Gnomad EAS

AF:

0.750

Gnomad SAS

AF:

0.681

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.565

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.550

AC:

60461

AN:

109836

Hom.:

12013

Cov.:

AF XY:

0.551

AC XY:

17717

AN XY:

32142

show subpopulations

African (AFR)

AF:

0.623

AC:

18810

AN:

30202

American (AMR)

AF:

0.554

AC:

5708

AN:

10305

Ashkenazi Jewish (ASJ)

AF:

0.574

AC:

1508

AN:

2629

East Asian (EAS)

AF:

0.749

AC:

2601

AN:

3474

South Asian (SAS)

AF:

0.678

AC:

1750

AN:

2580

European-Finnish (FIN)

AF:

0.507

AC:

2860

AN:

5637

Middle Eastern (MID)

AF:

0.670

AC:

138

AN:

206

European-Non Finnish (NFE)

AF:

0.491

AC:

25852

AN:

52638

Other (OTH)

AF:

0.571

AC:

853

AN:

1494

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

959

1918

2876

3835

4794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.519

Hom.:

4647

Bravo

AF:

0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.2

(source)

DANN

Benign

0.80

PhyloP100

0.061

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over