Genetic Variant SLC29A1:c.864+4C>T (chr6-44231465-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001372327.1(SLC29A1):c.864+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00393 in 1,578,214 control chromosomes in the GnomAD database, including 203 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 95 hom., cov: 32)

Exomes 𝑓: 0.0022 ( 108 hom. )

Consequence

SLC29A1
NM_001372327.1 splice_region, intron

Scores

Splicing: ADA: 0.00006634

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.87

Variant links:

Genes affected

SLC29A1 (HGNC:11003): (solute carrier family 29 member 1 (Augustine blood group)) This gene is a member of the equilibrative nucleoside transporter family. The gene encodes a transmembrane glycoprotein that localizes to the plasma and mitochondrial membranes and mediates the cellular uptake of nucleosides from the surrounding medium. The protein is categorized as an equilibrative (as opposed to concentrative) transporter that is sensitive to inhibition by nitrobenzylthioinosine (NBMPR). Nucleoside transporters are required for nucleotide synthesis in cells that lack de novo nucleoside synthesis pathways, and are also necessary for the uptake of cytotoxic nucleosides used for cancer and viral chemotherapies. Multiple alternatively spliced variants, encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

SLC29A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 6-44231465-C-T is Benign according to our data. Variant chr6-44231465-C-T is described in ClinVar as [Benign]. Clinvar id is 780626.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC29A1	NM_001372327.1 link	c.864+4C>T		splice_region_variant, intron_variant	Intron 9 of 12	ENST00000371755.9	NP_001359256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC29A1	ENST00000371755.9 link	c.864+4C>T		splice_region_variant, intron_variant	Intron 9 of 12	1	NM_001372327.1	ENSP00000360820.3		Q99808-1

Frequencies

GnomAD3 genomes

AF:

0.0199

AC:

3033

AN:

152092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0692

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00648

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000456

Gnomad OTH

AF:

0.0153

GnomAD3 exomes

AF:

0.00548

AC:

1254

AN:

228916

Hom.:

AF XY:

0.00387

AC XY:

477

AN XY:

123346

show subpopulations

Gnomad AFR exome

AF:

0.0732

Gnomad AMR exome

AF:

0.00459

Gnomad ASJ exome

AF:

0.000106

Gnomad EAS exome

AF:

0.0000558

Gnomad SAS exome

AF:

0.000246

Gnomad FIN exome

AF:

0.0000504

Gnomad NFE exome

AF:

0.000330

Gnomad OTH exome

AF:

0.00315

GnomAD4 exome

AF:

0.00222

AC:

3160

AN:

1426004

Hom.:

108

Cov.:

AF XY:

0.00190

AC XY:

1348

AN XY:

709630

show subpopulations

Gnomad4 AFR exome

AF:

0.0717

Gnomad4 AMR exome

AF:

0.00455

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.000202

Gnomad4 FIN exome

AF:

0.0000190

Gnomad4 NFE exome

AF:

0.000248

Gnomad4 OTH exome

AF:

0.00496

GnomAD4 genome

AF:

0.0200

AC:

3039

AN:

152210

Hom.:

Cov.:

AF XY:

0.0197

AC XY:

1468

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0692

Gnomad4 AMR

AF:

0.00647

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000456

Gnomad4 OTH

AF:

0.0151

Alfa

AF:

0.00494

Hom.:

Bravo

AF:

0.0229

Asia WGS

AF:

0.00462

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 05, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.0050

DANN

Benign

0.43

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000066

dbscSNV1_RF

Benign

0.018

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