Variant chr6-73594106-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_012434.5(SLC17A5):c.*971G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,412 control chromosomes in the GnomAD database, including 11,393 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 11393 hom., cov: 29)

Exomes 𝑓: 0.18 ( 0 hom. )

Consequence

SLC17A5
NM_012434.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -2.27

Variant links:

Genes affected

SLC17A5 (HGNC:10933): (solute carrier family 17 member 5) This gene encodes a membrane transporter that exports free sialic acids that have been cleaved off of cell surface lipids and proteins from lysosomes. Mutations in this gene cause sialic acid storage diseases, including infantile sialic acid storage disorder and and Salla disease, an adult form. [provided by RefSeq, Jul 2008]

SLC17A5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BP6

Variant 6-73594106-C-T is Benign according to our data. Variant chr6-73594106-C-T is described in ClinVar as [Benign]. Clinvar id is 357907.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A5	NM_012434.5 link	c.*971G>A		3_prime_UTR_variant	11/11	ENST00000355773.6	NP_036566.1	Q9NRA2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A5	ENST00000355773 link	c.*971G>A		3_prime_UTR_variant	11/11	1	NM_012434.5	ENSP00000348019.5		Q9NRA2-1

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57072

AN:

151272

Hom.:

11381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.0870

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.373

Gnomad OTH

AF:

0.364

GnomAD4 exome

AF:

0.182

AC:

AN:

Hom.:

Cov.:

AF XY:

0.143

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.377

AC:

57120

AN:

151390

Hom.:

11393

Cov.:

AF XY:

0.373

AC XY:

27566

AN XY:

73918

show subpopulations

Gnomad4 AFR

AF:

0.473

Gnomad4 AMR

AF:

0.289

Gnomad4 ASJ

AF:

0.401

Gnomad4 EAS

AF:

0.0868

Gnomad4 SAS

AF:

0.251

Gnomad4 FIN

AF:

0.361

Gnomad4 NFE

AF:

0.373

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.382

Hom.:

1451

Bravo

AF:

0.375

Asia WGS

AF:

0.179

AC:

625

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Sialic acid storage disease, severe infantile type

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Salla disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.39

DANN

Benign

0.58

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over