Variant 10-71319545-C-G 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.-420C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 407,542 control chromosomes in the GnomAD database, including 42,299 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 18124 hom., cov: 32)

Exomes 𝑓: 0.43 ( 24175 hom. )

Consequence

SLC29A3
NM_001363518.2 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.09

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:

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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=-0.81).

BP6

Variant 10-71319545-C-G is Benign according to our data. Variant chr10-71319545-C-G is described in ClinVar as [Benign]. Clinvar id is 1239908.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+235C>G		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+235C>G		intron_variant		1	NM_018344.6	ENSP00000362285.5		Q9BZD2-1

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72325

AN:

151844

Hom.:

18114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.451

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.401

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.450

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.408

Gnomad OTH

AF:

0.442

GnomAD4 exome

AF:

0.429

AC:

109742

AN:

255580

Hom.:

24175

Cov.:

AF XY:

0.427

AC XY:

56611

AN XY:

132530

show subpopulations

Gnomad4 AFR exome

AF:

0.640

Gnomad4 AMR exome

AF:

0.342

Gnomad4 ASJ exome

AF:

0.427

Gnomad4 EAS exome

AF:

0.425

Gnomad4 SAS exome

AF:

0.502

Gnomad4 FIN exome

AF:

0.459

Gnomad4 NFE exome

AF:

0.416

Gnomad4 OTH exome

AF:

0.437

GnomAD4 genome

AF:

0.476

AC:

72375

AN:

151962

Hom.:

18124

Cov.:

AF XY:

0.475

AC XY:

35300

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.645

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.431

Gnomad4 EAS

AF:

0.401

Gnomad4 SAS

AF:

0.456

Gnomad4 FIN

AF:

0.450

Gnomad4 NFE

AF:

0.408

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.449

Hom.:

1943

Bravo

AF:

0.473

Asia WGS

AF:

0.435

AC:

1512

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	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.8

DANN

Benign

0.69

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.

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