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GeneBe

2-27201040-C-T

Variant summary

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

The NM_021095.4(SLC5A6):c.1722G>A(p.Pro574=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,613,772 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0064 ( 12 hom., cov: 31)
Exomes 𝑓: 0.00075 ( 13 hom. )

Consequence

SLC5A6
NM_021095.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.304
Variant links:
Genes affected
SLC5A6 (HGNC:11041): (solute carrier family 5 member 6) Enables biotin transmembrane transporter activity and pantothenate transmembrane transporter activity. Involved in anion transmembrane transport and transport across blood-brain barrier. Located in 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=-0.67).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-27201040-C-T is Benign according to our data. Variant chr2-27201040-C-T is described in ClinVar as [Benign]. Clinvar id is 787001.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=-0.304 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 = 0.00639 (973/152198) while in subpopulation AFR AF= 0.0221 (918/41510). AF 95% confidence interval is 0.0209. There are 12 homozygotes in gnomad4. There are 479 alleles in male gnomad4 subpopulation. Median coverage is 31. 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
SLC5A6NM_021095.4 linkuse as main transcriptc.1722G>A p.Pro574= synonymous_variant 16/17 ENST00000310574.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC5A6ENST00000310574.8 linkuse as main transcriptc.1722G>A p.Pro574= synonymous_variant 16/171 NM_021095.4 P1
SLC5A6ENST00000408041.5 linkuse as main transcriptc.1722G>A p.Pro574= synonymous_variant 17/181 P1
SLC5A6ENST00000461757.1 linkuse as main transcriptn.1272G>A non_coding_transcript_exon_variant 2/32
SLC5A6ENST00000488743.6 linkuse as main transcriptn.2408G>A non_coding_transcript_exon_variant 15/172

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00640
AC:
974
AN:
152080
Hom.:
12
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0222
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00190
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00116
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00430
GnomAD3 exomes
AF:
0.00190
AC:
476
AN:
251186
Hom.:
3
AF XY:
0.00130
AC XY:
176
AN XY:
135746
show subpopulations
Gnomad AFR exome
AF:
0.0225
Gnomad AMR exome
AF:
0.00101
Gnomad ASJ exome
AF:
0.000597
Gnomad EAS exome
AF:
0.000924
Gnomad SAS exome
AF:
0.000818
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000114
Gnomad OTH exome
AF:
0.00245
GnomAD4 exome
AF:
0.000747
AC:
1092
AN:
1461574
Hom.:
13
Cov.:
31
AF XY:
0.000631
AC XY:
459
AN XY:
727082
show subpopulations
Gnomad4 AFR exome
AF:
0.0222
Gnomad4 AMR exome
AF:
0.00112
Gnomad4 ASJ exome
AF:
0.000498
Gnomad4 EAS exome
AF:
0.000756
Gnomad4 SAS exome
AF:
0.000766
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000657
Gnomad4 OTH exome
AF:
0.00189
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00639
AC:
973
AN:
152198
Hom.:
12
Cov.:
31
AF XY:
0.00644
AC XY:
479
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0221
Gnomad4 AMR
AF:
0.00190
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00116
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00426
Alfa
AF:
0.00168
Hom.:
6
Bravo
AF:
0.00730
Asia WGS
AF:
0.00202
AC:
7
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.000237

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 testingInvitaeDec 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
Cadd
Benign
5.2
Dann
Benign
0.45

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: rs61737378; hg19: chr2-27423908; API