rs1417210

Variant names:

• chr10-71376162-G-A
• rs1417210
• ENST00000642772.1:n.*211+351G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642772.1(SLC29A3):​n.*211+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 ENST00000642772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 19 publications found

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: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet
• dysosteosclerosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC29A3	XM_047425425.1	c.*26+351G>A		intron_variant	Intron 6 of 6		XP_047281381.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC29A3	ENST00000642772.1	n.*211+351G>A		intron_variant	Intron 4 of 4			ENSP00000495041.1
SLC29A3	ENST00000644895.1	n.*216+351G>A		intron_variant	Intron 5 of 5			ENSP00000493872.1

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

African (AFR) AF: 0.955 AC: 39705 AN: 41578

American (AMR) AF: 0.779 AC: 11922 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3192 AN: 3470

East Asian (EAS) AF: 0.687 AC: 3552 AN: 5172

South Asian (SAS) AF: 0.780 AC: 3761 AN: 4822

European-Finnish (FIN) AF: 0.877 AC: 9302 AN: 10612

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61694 AN: 68026

Other (OTH) AF: 0.899 AC: 1903 AN: 2116

Alfa AF: 0.898 Hom.: 181094

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
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1417210; hg19: chr10-73135919;