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GeneBe

rs9364554

Variant summary

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

The NM_021977.4(SLC22A3):c.975+1786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152014 control chromosomes in the gnomAD Genomes database, including 4174 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 0.21 ( 4174 hom., cov: 32)

Consequence

SLC22A3
NM_021977.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390

Links

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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=-0.88).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC22A3NM_021977.4 linkuse as main transcriptc.975+1786C>T intron_variant ENST00000275300.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC22A3ENST00000275300.3 linkuse as main transcriptc.975+1786C>T intron_variant 1 NM_021977.4 P1

Frequencies

GnomAD3 genomes
AF:
0.209
AC:
31817
AN:
152014
Hom.:
4174
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0631
Gnomad AMI
AF:
0.340
Gnomad AMR
AF:
0.216
Gnomad ASJ
AF:
0.193
Gnomad EAS
AF:
0.328
Gnomad SAS
AF:
0.274
Gnomad FIN
AF:
0.234
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.193
Alfa
AF:
0.266
Hom.:
12362
Bravo
AF:
0.200
Asia WGS
AF:
0.334
AC:
1159
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
1.7
Dann
Benign
0.53

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: rs9364554; hg19: chr6-160833664; COSMIC: COSV51710312; API