X-46599693-G-T

Position:

• chrX-46599693-G-T

Variant summary

Our verdict is Likely benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC9A7	NM_001257291.2	c.*7259C>A		3_prime_UTR_variant	17/17	ENST00000616978.5	NP_001244220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC9A7	ENST00000616978	c.*7259C>A		3_prime_UTR_variant	17/17	1	NM_001257291.2	ENSP00000480916.1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 60450 AN: 109786 Hom.: 12015 Cov.: 22 AF XY: 0.552 AC XY: 17702 AN XY: 32082

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

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

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.571

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6640; hg19: chrX-46459128;