Variant 10-71319390-G-A 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 ENST00000373189.6(SLC29A3):c.1+80G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 576,992 control chromosomes in the GnomAD database, including 57,931 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 18111 hom., cov: 32)

Exomes 𝑓: 0.43 ( 39820 hom. )

Consequence

SLC29A3
ENST00000373189.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.438

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:

LOC124902445 (HGNC:):

LOC124902445 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=-0.77).

BP6

Variant 10-71319390-G-A is Benign according to our data. Variant chr10-71319390-G-A is described in ClinVar as [Benign]. Clinvar id is 1220931.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+80G>A		intron_variant		ENST00000373189.6	NP_060814.4
LOC124902445	XR_007062183.1 linkuse as main transcript	n.102+172C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC29A3	ENST00000373189.6 linkuse as main transcript	c.1+80G>A		intron_variant		1	NM_018344.6	ENSP00000362285	P1	Q9BZD2-1

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72282

AN:

151732

Hom.:

18101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.452

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.408

Gnomad OTH

AF:

0.442

GnomAD4 exome

AF:

0.429

AC:

182200

AN:

425144

Hom.:

39820

Cov.:

AF XY:

0.427

AC XY:

99029

AN XY:

231730

show subpopulations

Gnomad4 AFR exome

AF:

0.649

Gnomad4 AMR exome

AF:

0.383

Gnomad4 ASJ exome

AF:

0.425

Gnomad4 EAS exome

AF:

0.426

Gnomad4 SAS exome

AF:

0.464

Gnomad4 FIN exome

AF:

0.454

Gnomad4 NFE exome

AF:

0.414

Gnomad4 OTH exome

AF:

0.437

GnomAD4 genome

AF:

0.476

AC:

72332

AN:

151848

Hom.:

18111

Cov.:

AF XY:

0.476

AC XY:

35307

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.645

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.431

Gnomad4 EAS

AF:

0.400

Gnomad4 SAS

AF:

0.456

Gnomad4 FIN

AF:

0.451

Gnomad4 NFE

AF:

0.408

Gnomad4 OTH

AF:

0.441

Alfa

AF:

0.434

Hom.:

1778

Bravo

AF:

0.473

Asia WGS

AF:

0.434

AC:

1508

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

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	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 48% of patients studied by a panel of primary immunodeficiencies. Number of patients: 42. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

8.6

DANN

Benign

0.89

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