rs1901512

Variant summary

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

The NM_173488.5(SLCO6A1):​c.2017+517A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,938 control chromosomes in the GnomAD database, including 32,505 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 0.65 ( 32505 hom., cov: 31)

Consequence

SLCO6A1
NM_173488.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.137
Variant links:
Genes affected
SLCO6A1 (HGNC:23613): (solute carrier organic anion transporter family member 6A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLCO6A1NM_173488.5 linkuse as main transcriptc.2017+517A>G intron_variant ENST00000506729.6 NP_775759.3 Q86UG4-1A0A140VJU7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLCO6A1ENST00000506729.6 linkuse as main transcriptc.2017+517A>G intron_variant 1 NM_173488.5 ENSP00000421339.1 Q86UG4-1

Frequencies

GnomAD3 genomes
AF:
0.651
AC:
98854
AN:
151820
Hom.:
32486
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.611
Gnomad AMI
AF:
0.722
Gnomad AMR
AF:
0.586
Gnomad ASJ
AF:
0.718
Gnomad EAS
AF:
0.458
Gnomad SAS
AF:
0.609
Gnomad FIN
AF:
0.747
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.689
Gnomad OTH
AF:
0.637
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.651
AC:
98915
AN:
151938
Hom.:
32505
Cov.:
31
AF XY:
0.653
AC XY:
48474
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.611
Gnomad4 AMR
AF:
0.585
Gnomad4 ASJ
AF:
0.718
Gnomad4 EAS
AF:
0.458
Gnomad4 SAS
AF:
0.609
Gnomad4 FIN
AF:
0.747
Gnomad4 NFE
AF:
0.689
Gnomad4 OTH
AF:
0.632
Alfa
AF:
0.663
Hom.:
8172
Bravo
AF:
0.641
Asia WGS
AF:
0.531
AC:
1841
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.5
DANN
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1901512; hg19: chr5-101723875; API