chr3-143707136-G-A

Position:

• chr3-143707136-G-A

Variant summary

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

The NM_173653.4(SLC9A9):​c.534-13829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 152,002 control chromosomes in the GnomAD database, including 34,111 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 0.67 (34111 hom., cov: 31)
• Consequence: SLC9A9 NM_173653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9A9	NM_173653.4	c.534-13829C>T		intron_variant		ENST00000316549.11
SLC9A9	XM_011512704.4	c.534-13829C>T		intron_variant
SLC9A9	XM_017006202.3	c.534-13829C>T		intron_variant
SLC9A9	XM_017006203.2	c.183-13829C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9A9	ENST00000316549.11	c.534-13829C>T		intron_variant		1	NM_173653.4	P1
SLC9A9	ENST00000474727.2	c.*145-13829C>T		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101204 AN: 151886 Hom.: 34085 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.666 AC: 101283 AN: 152002 Hom.: 34111 Cov.: 31 AF XY: 0.661 AC XY: 49081 AN XY: 74278

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.662

Alfa AF: 0.731 Hom.: 11157

Bravo AF: 0.667

Asia WGS AF: 0.536 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.066
DANN	Benign	0.67

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: rs9828519; hg19: chr3-143425978;