chrX-46599693-G-T

Variant names:

• chrX-46599693-G-T
• rs6640
• NM_001257291.2:c.*7259C>A

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 3 publications found

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: Unknown, XL Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• non-syndromic X-linked intellectual disability

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A7	NM_001257291.2	c.*7259C>A		3_prime_UTR_variant	Exon 17 of 17	ENST00000616978.5	NP_001244220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A7	ENST00000616978.5	c.*7259C>A		3_prime_UTR_variant	Exon 17 of 17	1	NM_001257291.2	ENSP00000480916.1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 60450 AN: 109786 Hom.: 12015 Cov.: 22

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: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.550 AC: 60461 AN: 109836 Hom.: 12013 Cov.: 22 AF XY: 0.551 AC XY: 17717 AN XY: 32142

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

Alfa AF: 0.519 Hom.: 4647

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.2
DANN	Benign	0.80
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs6640; hg19: chrX-46459128;