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GeneBe

rs377551

Variant summary

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

The NM_021977.4(SLC22A3):c.429+11853G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,968 control chromosomes in the GnomAD database, including 9,979 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 0.35 ( 9979 hom., cov: 32)

Consequence

SLC22A3
NM_021977.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.15
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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC22A3NM_021977.4 linkuse as main transcriptc.429+11853G>A intron_variant ENST00000275300.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC22A3ENST00000275300.3 linkuse as main transcriptc.429+11853G>A intron_variant 1 NM_021977.4 P1

Frequencies

GnomAD3 genomes
AF:
0.346
AC:
52513
AN:
151850
Hom.:
9947
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.521
Gnomad AMI
AF:
0.195
Gnomad AMR
AF:
0.237
Gnomad ASJ
AF:
0.368
Gnomad EAS
AF:
0.305
Gnomad SAS
AF:
0.253
Gnomad FIN
AF:
0.286
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.283
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.346
AC:
52598
AN:
151968
Hom.:
9979
Cov.:
32
AF XY:
0.342
AC XY:
25424
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.522
Gnomad4 AMR
AF:
0.236
Gnomad4 ASJ
AF:
0.368
Gnomad4 EAS
AF:
0.305
Gnomad4 SAS
AF:
0.254
Gnomad4 FIN
AF:
0.286
Gnomad4 NFE
AF:
0.283
Gnomad4 OTH
AF:
0.350
Alfa
AF:
0.297
Hom.:
7771
Bravo
AF:
0.354
Asia WGS
AF:
0.314
AC:
1092
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
0.098
Dann
Benign
0.59

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: rs377551; hg19: chr6-160781733; API