Menu
GeneBe

12-21300490-G-A

Variant summary

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

The NM_001386879.1(SLCO1A2):c.768C>T(p.Asn256=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00238 in 1,613,398 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 46 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 40 hom. )

Consequence

SLCO1A2
NM_001386879.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.22
Variant links:
Genes affected
SLCO1A2 (HGNC:10956): (solute carrier organic anion transporter family member 1A2) This gene encodes a sodium-independent transporter which mediates cellular uptake of organic ions in the liver. Its substrates include bile acids, bromosulphophthalein, and some steroidal compounds. The protein is a member of the SLC21A family of solute carriers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2008]

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=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 12-21300490-G-A is Benign according to our data. Variant chr12-21300490-G-A is described in ClinVar as [Benign]. Clinvar id is 788577.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=1.22 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1945/152120) while in subpopulation AFR AF= 0.0442 (1834/41490). AF 95% confidence interval is 0.0425. There are 46 homozygotes in gnomad4. There are 947 alleles in male gnomad4 subpopulation. Median coverage is 32. 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 45 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO1A2NM_001386879.1 linkuse as main transcriptc.768C>T p.Asn256= synonymous_variant 8/15 ENST00000683939.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO1A2ENST00000683939.1 linkuse as main transcriptc.768C>T p.Asn256= synonymous_variant 8/15 NM_001386879.1 P1P46721-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0127
AC:
1932
AN:
152002
Hom.:
45
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0440
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00518
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00955
GnomAD3 exomes
AF:
0.00337
AC:
845
AN:
250416
Hom.:
13
AF XY:
0.00251
AC XY:
340
AN XY:
135310
show subpopulations
Gnomad AFR exome
AF:
0.0451
Gnomad AMR exome
AF:
0.00230
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000654
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000203
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00129
AC:
1891
AN:
1461278
Hom.:
40
Cov.:
31
AF XY:
0.00110
AC XY:
800
AN XY:
726918
show subpopulations
Gnomad4 AFR exome
AF:
0.0446
Gnomad4 AMR exome
AF:
0.00271
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000928
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000112
Gnomad4 OTH exome
AF:
0.00227
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0128
AC:
1945
AN:
152120
Hom.:
46
Cov.:
32
AF XY:
0.0127
AC XY:
947
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0442
Gnomad4 AMR
AF:
0.00518
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00945
Alfa
AF:
0.00333
Hom.:
13
Bravo
AF:
0.0147
Asia WGS
AF:
0.00404
AC:
14
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000297

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 13, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
14
Dann
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs11568554; hg19: chr12-21453424; API