rs1417210

Positions:

• chr10-71376162-G-A
• chr10-71376162-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047425425.1(SLC29A3):​c.*26+351G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,302 control chromosomes in the GnomAD database, including 61,372 homozygotes. 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: 𝑓 0.89 (61372 hom., cov: 33)
• Consequence: SLC29A3 XM_047425425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC29A3	XM_047425425.1	c.*26+351G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC29A3	ENST00000642772.1	c.*211+351G>A		intron_variant, NMD_transcript_variant
SLC29A3	ENST00000644895.1	c.*216+351G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.894 AC: 136093 AN: 152184 Hom.: 61328 Cov.: 33

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.903

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.894 AC: 136191 AN: 152302 Hom.: 61372 Cov.: 33 AF XY: 0.888 AC XY: 66111 AN XY: 74472

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.899

Alfa AF: 0.898 Hom.: 77526

Bravo AF: 0.889

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.42
DANN	Benign	0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1417210; hg19: chr10-73135919;