Variant 10-71319472-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001363518.2(SLC29A3):c.-493T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 441,496 control chromosomes in the GnomAD database, including 46,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 18186 hom., cov: 32)

Exomes 𝑓: 0.44 ( 28074 hom. )

Consequence

SLC29A3
NM_001363518.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.101

Variant links:

Genes affected

SLC29A3 (HGNC:23096): (solute carrier family 29 member 3) This gene encodes a nucleoside transporter. The encoded protein plays a role in cellular uptake of nucleosides, nucleobases, and their related analogs. Mutations in this gene have been associated with H syndrome, which is characterized by cutaneous hyperpigmentation and hypertrichosis, hepatosplenomegaly, heart anomalies, and hypogonadism. A related disorder, PHID (pigmented hypertrichosis with insulin-dependent diabetes mellitus), has also been associated with mutations at this locus. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2010]

SLC29A3 links:

SLC29A3 (HGNC:):

SLC29A3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 10-71319472-T-C is Benign according to our data. Variant chr10-71319472-T-C is described in ClinVar as [Benign]. Clinvar id is 1272485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC29A3	NM_018344.6 linkuse as main transcript	c.1+162T>C		intron_variant		ENST00000373189.6	NP_060814.4	Q9BZD2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC29A3	ENST00000373189.6 linkuse as main transcript	c.1+162T>C		intron_variant		1	NM_018344.6	ENSP00000362285.5		Q9BZD2-1

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72482

AN:

151736

Hom.:

18176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.449

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.464

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.442

GnomAD4 exome

AF:

0.437

AC:

126431

AN:

289642

Hom.:

28074

Cov.:

AF XY:

0.436

AC XY:

66680

AN XY:

152958

show subpopulations

Gnomad4 AFR exome

AF:

0.641

Gnomad4 AMR exome

AF:

0.347

Gnomad4 ASJ exome

AF:

0.430

Gnomad4 EAS exome

AF:

0.425

Gnomad4 SAS exome

AF:

0.503

Gnomad4 FIN exome

AF:

0.477

Gnomad4 NFE exome

AF:

0.421

Gnomad4 OTH exome

AF:

0.444

GnomAD4 genome

AF:

0.478

AC:

72532

AN:

151854

Hom.:

18186

Cov.:

AF XY:

0.477

AC XY:

35435

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.646

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.431

Gnomad4 EAS

AF:

0.400

Gnomad4 SAS

AF:

0.456

Gnomad4 FIN

AF:

0.464

Gnomad4 NFE

AF:

0.409

Gnomad4 OTH

AF:

0.441

Alfa

AF:

0.431

Hom.:

2911

Bravo

AF:

0.473

Asia WGS

AF:

0.437

AC:

1520

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

5.5

DANN

Benign

0.75

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