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GeneBe

rs1501630

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173653.4(SLC9A9):​c.1604+38110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,202 control chromosomes in the GnomAD database, including 37,736 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 0.69 ( 37736 hom., cov: 33)

Consequence

SLC9A9
NM_173653.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.900
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC9A9NM_173653.4 linkuse as main transcriptc.1604+38110G>A intron_variant ENST00000316549.11
SLC9A9XM_011512703.4 linkuse as main transcriptc.956+38110G>A intron_variant
SLC9A9XM_017006202.3 linkuse as main transcriptc.1711+38003G>A intron_variant
SLC9A9XM_017006203.2 linkuse as main transcriptc.1253+38110G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC9A9ENST00000316549.11 linkuse as main transcriptc.1604+38110G>A intron_variant 1 NM_173653.4 P1

Frequencies

GnomAD3 genomes
AF:
0.688
AC:
104629
AN:
152086
Hom.:
37682
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.909
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.647
Gnomad ASJ
AF:
0.569
Gnomad EAS
AF:
0.430
Gnomad SAS
AF:
0.500
Gnomad FIN
AF:
0.769
Gnomad MID
AF:
0.570
Gnomad NFE
AF:
0.591
Gnomad OTH
AF:
0.673
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.688
AC:
104736
AN:
152202
Hom.:
37736
Cov.:
33
AF XY:
0.690
AC XY:
51345
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.910
Gnomad4 AMR
AF:
0.646
Gnomad4 ASJ
AF:
0.569
Gnomad4 EAS
AF:
0.430
Gnomad4 SAS
AF:
0.502
Gnomad4 FIN
AF:
0.769
Gnomad4 NFE
AF:
0.591
Gnomad4 OTH
AF:
0.670
Alfa
AF:
0.643
Hom.:
8651
Bravo
AF:
0.691
Asia WGS
AF:
0.527
AC:
1837
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.49
DANN
Benign
0.37

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1501630; hg19: chr3-143044216; API