GeneBe

10-71319390-G-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001363518.2(SLC29A3):​c.-575G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SLC29A3
NM_001363518.2 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.438

Publications

3 publications found
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 Gene-Disease associations (from GenCC):
  • H syndrome
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen
  • dysosteosclerosis
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363518.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC29A3
NM_018344.6
MANE Select
c.1+80G>C
intron
N/ANP_060814.4
SLC29A3
NM_001363518.2
c.-575G>C
5_prime_UTR
Exon 1 of 6NP_001350447.1A0A2R8YDR8
SLC29A3
NM_001174098.2
c.1+80G>C
intron
N/ANP_001167569.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC29A3
ENST00000373189.6
TSL:1 MANE Select
c.1+80G>C
intron
N/AENSP00000362285.5Q9BZD2-1
SLC29A3
ENST00000479577.2
TSL:2
c.-575G>C
5_prime_UTR
Exon 1 of 6ENSP00000493995.1A0A2R8YDR8
SLC29A3
ENST00000642198.1
n.-575G>C
non_coding_transcript_exon
Exon 1 of 6ENSP00000494827.1A0A2R8Y5U2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
425474
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
231912
African (AFR)
AF:
0.00
AC:
0
AN:
9210
American (AMR)
AF:
0.00
AC:
0
AN:
15550
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13634
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24800
South Asian (SAS)
AF:
0.00
AC:
0
AN:
45314
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
30224
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1978
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
260100
Other (OTH)
AF:
0.00
AC:
0
AN:
24664
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
1778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
8.4
DANN
Benign
0.76
PhyloP100
0.44
PromoterAI
-0.080
Neutral

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

Other links and lift over

dbSNP: rs17525188; hg19: chr10-73079147; API