rs956062

Positions:

• chr3-143692284-G-A
• chr3-143692284-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173653.4(SLC9A9):​c.649+908C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,864 control chromosomes in the GnomAD database, including 14,344 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 0.43 (14344 hom., cov: 33)
• Consequence: SLC9A9 NM_173653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC9A9	NM_173653.4	c.649+908C>T		intron_variant		ENST00000316549.11	NP_775924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC9A9	ENST00000316549.11	c.649+908C>T		intron_variant		1	NM_173653.4	ENSP00000320246	P1
SLC9A9	ENST00000483124.1	n.186+908C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65564 AN: 151746 Hom.: 14332 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.432 AC: 65605 AN: 151864 Hom.: 14344 Cov.: 33 AF XY: 0.435 AC XY: 32291 AN XY: 74222

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.451

Alfa AF: 0.425 Hom.: 1737

Bravo AF: 0.431

Asia WGS AF: 0.530 AC: 1837 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.9
DANN	Benign	0.63

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

Other links and lift over

dbSNP: rs956062; hg19: chr3-143411126;