chr3-143331660-T-C

Position:

• chr3-143331660-T-C

Variant summary

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

The NM_173653.4(SLC9A9):​c.1604+31824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,020 control chromosomes in the GnomAD database, including 9,508 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 0.34 (9508 hom., cov: 32)
• Consequence: SLC9A9 NM_173653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC9A9	NM_173653.4	c.1604+31824A>G		intron_variant		ENST00000316549.11	NP_775924.1
SLC9A9	XM_011512703.4	c.956+31824A>G		intron_variant			XP_011511005.1
SLC9A9	XM_017006202.3	c.1711+31717A>G		intron_variant			XP_016861691.1
SLC9A9	XM_017006203.2	c.1253+31824A>G		intron_variant			XP_016861692.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC9A9	ENST00000316549.11	c.1604+31824A>G		intron_variant		1	NM_173653.4	ENSP00000320246	P1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51241 AN: 151902 Hom.: 9503 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.337 AC: 51281 AN: 152020 Hom.: 9508 Cov.: 32 AF XY: 0.340 AC XY: 25292 AN XY: 74310

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.308

Alfa AF: 0.264 Hom.: 9295

Bravo AF: 0.347

Asia WGS AF: 0.263 AC: 914 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	0.62
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9332458; hg19: chr3-143050502;