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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 152,132 control chromosomes in the GnomAD database, including 4,172 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 ( 4172 hom., cov: 32)

Consequence

SLC22A3
NM_021977.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390
Variant links:
Genes affected
SLC22A3 (HGNC:10967): (solute carrier family 22 member 3) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. [provided by RefSeq, Jul 2008]

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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
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.209
AC:
31822
AN:
152132
Hom.:
4172
Cov.:
32
AF XY:
0.207
AC XY:
15430
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.0632
Gnomad4 AMR
AF:
0.216
Gnomad4 ASJ
AF:
0.193
Gnomad4 EAS
AF:
0.327
Gnomad4 SAS
AF:
0.273
Gnomad4 FIN
AF:
0.234
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.196
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
3.1
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