chr17-6686176-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_177550.5(SLC13A5):​c.*31T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00594 in 1,613,602 control chromosomes in the GnomAD database, including 429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 213 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 216 hom. )

Consequence

SLC13A5
NM_177550.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.16
Variant links:
Genes affected
SLC13A5 (HGNC:23089): (solute carrier family 13 member 5) This gene encodes a protein belonging to the solute carrier family 13 group of proteins. This family member is a sodium-dependent citrate cotransporter that may regulate metabolic processes. Mutations in this gene cause early infantile epileptic encephalopathy 25. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]
C17orf100 (HGNC:34494): (chromosome 17 open reading frame 100)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 17-6686176-A-G is Benign according to our data. Variant chr17-6686176-A-G is described in ClinVar as [Benign]. Clinvar id is 1230912.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC13A5NM_177550.5 linkuse as main transcriptc.*31T>C 3_prime_UTR_variant 12/12 ENST00000433363.7
SLC13A5NM_001143838.3 linkuse as main transcriptc.*31T>C 3_prime_UTR_variant 11/11
SLC13A5NM_001284509.2 linkuse as main transcriptc.*31T>C 3_prime_UTR_variant 12/12
SLC13A5NM_001284510.2 linkuse as main transcriptc.*31T>C 3_prime_UTR_variant 11/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC13A5ENST00000433363.7 linkuse as main transcriptc.*31T>C 3_prime_UTR_variant 12/121 NM_177550.5 P1Q86YT5-1
ENST00000634558.1 linkuse as main transcriptn.511-3700A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0296
AC:
4501
AN:
152072
Hom.:
211
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0128
Gnomad ASJ
AF:
0.00116
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.000823
Gnomad OTH
AF:
0.0263
GnomAD3 exomes
AF:
0.00840
AC:
2110
AN:
251214
Hom.:
70
AF XY:
0.00619
AC XY:
840
AN XY:
135764
show subpopulations
Gnomad AFR exome
AF:
0.104
Gnomad AMR exome
AF:
0.00782
Gnomad ASJ exome
AF:
0.00179
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000783
Gnomad OTH exome
AF:
0.00587
GnomAD4 exome
AF:
0.00348
AC:
5083
AN:
1461412
Hom.:
216
Cov.:
31
AF XY:
0.00295
AC XY:
2148
AN XY:
727012
show subpopulations
Gnomad4 AFR exome
AF:
0.106
Gnomad4 AMR exome
AF:
0.00895
Gnomad4 ASJ exome
AF:
0.00161
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000197
Gnomad4 FIN exome
AF:
0.0000562
Gnomad4 NFE exome
AF:
0.000535
Gnomad4 OTH exome
AF:
0.00736
GnomAD4 genome
AF:
0.0296
AC:
4505
AN:
152190
Hom.:
213
Cov.:
32
AF XY:
0.0287
AC XY:
2137
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.0128
Gnomad4 ASJ
AF:
0.00116
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000824
Gnomad4 OTH
AF:
0.0260
Alfa
AF:
0.00848
Hom.:
53
Bravo
AF:
0.0341
Asia WGS
AF:
0.00520
AC:
18
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 testingGeneDxJun 25, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.4
DANN
Benign
0.76
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs16956120; hg19: chr17-6589495; API