NM_173653.4:c.534-15400C>G

Variant names:

• chr3-143708707-G-C
• rs1562495
• NM_173653.4:c.534-15400C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173653.4(SLC9A9):​c.534-15400C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,972 control chromosomes in the GnomAD database, including 26,821 homozygotes. 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 0.59 (26821 hom., cov: 31)
• Consequence: SLC9A9 NM_173653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 0 publications found

Genes affected

SLC9A9 (HGNC:20653): (solute carrier family 9 member A9) This gene encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein family. The encoded protein localizes the to the late recycling endosomes and may play an important role in maintaining cation homeostasis. Mutations in this gene are associated with autism susceptibility 16 and attention-deficit/hyperactivity disorder. [provided by RefSeq, Mar 2012]

SLC9A9 Gene-Disease associations (from GenCC):

• autism, susceptibility to, 16

  Inheritance: AD Classification: LIMITED Submitted by: G2P
• autism spectrum disorder

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A9	NM_173653.4	c.534-15400C>G		intron_variant	Intron 4 of 15	ENST00000316549.11	NP_775924.1
SLC9A9	XM_017006202.3	c.534-15400C>G		intron_variant	Intron 4 of 14		XP_016861691.1
SLC9A9	XM_017006203.2	c.183-15400C>G		intron_variant	Intron 3 of 14		XP_016861692.1
SLC9A9	XM_011512704.4	c.534-15400C>G		intron_variant	Intron 4 of 9		XP_011511006.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A9	ENST00000316549.11	c.534-15400C>G		intron_variant	Intron 4 of 15	1	NM_173653.4	ENSP00000320246.6
SLC9A9	ENST00000474727.2	n.*145-15400C>G		intron_variant	Intron 3 of 3	4		ENSP00000419090.2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89799 AN: 151854 Hom.: 26803 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.605

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.591 AC: 89869 AN: 151972 Hom.: 26821 Cov.: 31 AF XY: 0.586 AC XY: 43552 AN XY: 74282

African (AFR) AF: 0.593 AC: 24560 AN: 41410

American (AMR) AF: 0.597 AC: 9113 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2123 AN: 3468

East Asian (EAS) AF: 0.405 AC: 2090 AN: 5164

South Asian (SAS) AF: 0.519 AC: 2501 AN: 4818

European-Finnish (FIN) AF: 0.593 AC: 6260 AN: 10556

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41407 AN: 67982

Other (OTH) AF: 0.603 AC: 1274 AN: 2114

Alfa AF: 0.600 Hom.: 3395

Bravo AF: 0.593

Asia WGS AF: 0.497 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.83
DANN	Benign	0.44
PhyloP100		0.034
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1562495; hg19: chr3-143427549;