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GeneBe

11-64556035-C-T

Variant summary

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

The NM_018484.4(SLC22A11):c.36C>T(p.Gly12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,612,884 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0061 ( 12 hom., cov: 32)
Exomes 𝑓: 0.00064 ( 10 hom. )

Consequence

SLC22A11
NM_018484.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.84
Variant links:
Genes affected
SLC22A11 (HGNC:18120): (solute carrier family 22 member 11) The protein encoded by this gene is involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and is found mainly in the kidney and in the placenta, where it may act to prevent potentially harmful organic anions from reaching the fetus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

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=-0.74).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-64556035-C-T is Benign according to our data. Variant chr11-64556035-C-T is described in ClinVar as [Benign]. Clinvar id is 711553.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=-1.84 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 = 0.00613 (934/152324) while in subpopulation AFR AF= 0.0206 (856/41562). AF 95% confidence interval is 0.0195. There are 12 homozygotes in gnomad4. There are 422 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 12 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC22A11NM_018484.4 linkuse as main transcriptc.36C>T p.Gly12= synonymous_variant 1/10 ENST00000301891.9
SLC22A11NM_001307985.2 linkuse as main transcriptc.36C>T p.Gly12= synonymous_variant 1/8
SLC22A11XM_011545167.2 linkuse as main transcriptc.-260C>T 5_prime_UTR_variant 1/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC22A11ENST00000301891.9 linkuse as main transcriptc.36C>T p.Gly12= synonymous_variant 1/101 NM_018484.4 P1Q9NSA0-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00614
AC:
934
AN:
152206
Hom.:
12
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0206
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00392
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00334
GnomAD3 exomes
AF:
0.00161
AC:
403
AN:
250094
Hom.:
5
AF XY:
0.00118
AC XY:
159
AN XY:
135248
show subpopulations
Gnomad AFR exome
AF:
0.0207
Gnomad AMR exome
AF:
0.00145
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000882
Gnomad OTH exome
AF:
0.000819
GnomAD4 exome
AF:
0.000635
AC:
928
AN:
1460560
Hom.:
10
Cov.:
31
AF XY:
0.000564
AC XY:
410
AN XY:
726626
show subpopulations
Gnomad4 AFR exome
AF:
0.0217
Gnomad4 AMR exome
AF:
0.00139
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000477
Gnomad4 OTH exome
AF:
0.00134
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00613
AC:
934
AN:
152324
Hom.:
12
Cov.:
32
AF XY:
0.00567
AC XY:
422
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.0206
Gnomad4 AMR
AF:
0.00392
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00243
Hom.:
3
Bravo
AF:
0.00697
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000119

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 testingInvitaeMay 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
Cadd
Benign
1.2
Dann
Benign
0.48

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: rs72559736; hg19: chr11-64323507; API