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GeneBe

6-25798815-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2

The NM_005074.5(SLC17A1):c.1374G>A(p.Trp458Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000614 in 1,609,450 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00032 ( 4 hom. )

Consequence

SLC17A1
NM_005074.5 stop_gained

Scores

3
3
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.97
Variant links:
Genes affected
SLC17A1 (HGNC:10929): (solute carrier family 17 member 1) Predicted to enable sialic acid transmembrane transporter activity. Involved in urate metabolic process and urate transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Stoplost variant in NM_005074.5 Downstream stopcodon found after 145 codons.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-25798815-C-T is Benign according to our data. Variant chr6-25798815-C-T is described in ClinVar as [Benign]. Clinvar id is 716025.Status of the report is criteria_provided_single_submitter, 1 stars.
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 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC17A1NM_005074.5 linkuse as main transcriptc.1374G>A p.Trp458Ter stop_gained 12/13 ENST00000244527.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC17A1ENST00000244527.10 linkuse as main transcriptc.1374G>A p.Trp458Ter stop_gained 12/135 NM_005074.5 P1Q14916-1
SLC17A1ENST00000468082.1 linkuse as main transcriptc.1212G>A p.Trp404Ter stop_gained 10/101 Q14916-2
SLC17A1ENST00000476801.5 linkuse as main transcriptc.1374G>A p.Trp458Ter stop_gained 12/122 P1Q14916-1
SLC17A1ENST00000377886.6 linkuse as main transcriptc.*625G>A 3_prime_UTR_variant, NMD_transcript_variant 11/125

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00345
AC:
524
AN:
152076
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0115
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00216
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00641
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.000872
AC:
219
AN:
251144
Hom.:
1
AF XY:
0.000479
AC XY:
65
AN XY:
135746
show subpopulations
Gnomad AFR exome
AF:
0.0118
Gnomad AMR exome
AF:
0.000579
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000352
Gnomad OTH exome
AF:
0.000490
GnomAD4 exome
AF:
0.000318
AC:
464
AN:
1457254
Hom.:
4
Cov.:
31
AF XY:
0.000269
AC XY:
195
AN XY:
724720
show subpopulations
Gnomad4 AFR exome
AF:
0.0115
Gnomad4 AMR exome
AF:
0.000559
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000902
Gnomad4 OTH exome
AF:
0.000715
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00345
AC:
525
AN:
152196
Hom.:
4
Cov.:
32
AF XY:
0.00297
AC XY:
221
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.0115
Gnomad4 AMR
AF:
0.00216
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.000459
Hom.:
1
Bravo
AF:
0.00372
ESP6500AA
AF:
0.0107
AC:
47
ESP6500EA
AF:
0.00
AC:
0
ExAC
?
    Exome Aggregation Consortium database
AF:
0.000997
AC:
121
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

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 testingInvitaeApr 02, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.24
D
BayesDel_noAF
Pathogenic
0.58
Cadd
Pathogenic
37
Dann
Uncertain
0.99
Eigen
Pathogenic
0.71
Eigen_PC
Uncertain
0.54
FATHMM_MKL
Uncertain
0.89
D
MutationTaster
Benign
1.0
D;D;D;D
Vest4
0.71
GERP RS
4.0

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: rs74521692; hg19: chr6-25799043; API