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GeneBe

5-102458463-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_173488.5(SLCO6A1):c.1050T>C(p.Arg350=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 1,612,604 control chromosomes in the GnomAD database, including 166 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0082 ( 12 hom., cov: 32)
Exomes 𝑓: 0.014 ( 154 hom. )

Consequence

SLCO6A1
NM_173488.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.517
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-102458463-A-G is Benign according to our data. Variant chr5-102458463-A-G is described in ClinVar as [Benign]. Clinvar id is 777976.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.517 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.014 (20402/1460322) while in subpopulation NFE AF= 0.0169 (18736/1111170). AF 95% confidence interval is 0.0167. There are 154 homozygotes in gnomad4_exome. There are 9781 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 12 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO6A1NM_173488.5 linkuse as main transcriptc.1050T>C p.Arg350= synonymous_variant 6/14 ENST00000506729.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO6A1ENST00000506729.6 linkuse as main transcriptc.1050T>C p.Arg350= synonymous_variant 6/141 NM_173488.5 P1Q86UG4-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00824
AC:
1254
AN:
152164
Hom.:
12
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00222
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00406
Gnomad ASJ
AF:
0.00374
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00539
Gnomad FIN
AF:
0.00339
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0148
Gnomad OTH
AF:
0.00813
GnomAD3 exomes
AF:
0.00916
AC:
2296
AN:
250652
Hom.:
12
AF XY:
0.00912
AC XY:
1236
AN XY:
135490
show subpopulations
Gnomad AFR exome
AF:
0.00259
Gnomad AMR exome
AF:
0.00454
Gnomad ASJ exome
AF:
0.00397
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00419
Gnomad FIN exome
AF:
0.00519
Gnomad NFE exome
AF:
0.0154
Gnomad OTH exome
AF:
0.0116
GnomAD4 exome
AF:
0.0140
AC:
20402
AN:
1460322
Hom.:
154
Cov.:
30
AF XY:
0.0135
AC XY:
9781
AN XY:
726458
show subpopulations
Gnomad4 AFR exome
AF:
0.00188
Gnomad4 AMR exome
AF:
0.00438
Gnomad4 ASJ exome
AF:
0.00395
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.00370
Gnomad4 FIN exome
AF:
0.00626
Gnomad4 NFE exome
AF:
0.0169
Gnomad4 OTH exome
AF:
0.0106
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00823
AC:
1253
AN:
152282
Hom.:
12
Cov.:
32
AF XY:
0.00727
AC XY:
541
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.00221
Gnomad4 AMR
AF:
0.00406
Gnomad4 ASJ
AF:
0.00374
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00519
Gnomad4 FIN
AF:
0.00339
Gnomad4 NFE
AF:
0.0148
Gnomad4 OTH
AF:
0.00805
Alfa
AF:
0.0137
Hom.:
20
Bravo
AF:
0.00842
Asia WGS
AF:
0.00144
AC:
5
AN:
3476
EpiCase
AF:
0.0124
EpiControl
AF:
0.0145

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.37
Dann
Benign
0.41

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: rs114933736; hg19: chr5-101794167; API