Genetic Variant NM_001372327.1:c.-52+542A>C (chr6-44224183-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001372327.1(SLC29A1):c.-52+542A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,060 control chromosomes in the GnomAD database, including 55,202 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 0.85 ( 55202 hom., cov: 30)

Consequence

SLC29A1
NM_001372327.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.231

Publications

20 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372327.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC29A1	NM_001372327.1	MANE Select	c.-52+542A>C	intron	N/A	NP_001359256.1
SLC29A1	NM_001304462.2		c.186+2498A>C	intron	N/A	NP_001291391.1
SLC29A1	NM_001304465.2		c.25-3077A>C	intron	N/A	NP_001291394.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC29A1	ENST00000371755.9	TSL:1 MANE Select	c.-52+542A>C	intron	N/A	ENSP00000360820.3
SLC29A1	ENST00000393844.7	TSL:1	c.-51-3080A>C	intron	N/A	ENSP00000377427.1
SLC29A1	ENST00000371740.10	TSL:1	c.-159+542A>C	intron	N/A	ENSP00000360805.6

Frequencies

GnomAD3 genomes

AF:

0.848

AC:

128879

AN:

151942

Hom.:

55143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.963

Gnomad AMI

AF:

0.666

Gnomad AMR

AF:

0.757

Gnomad ASJ

AF:

0.866

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.782

Gnomad FIN

AF:

0.877

Gnomad MID

AF:

0.915

Gnomad NFE

AF:

0.810

Gnomad OTH

AF:

0.859

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

GnomAD4 genome

AF:

0.848

AC:

128995

AN:

152060

Hom.:

55202

Cov.:

AF XY:

0.847

AC XY:

62949

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.963

AC:

39939

AN:

41478

American (AMR)

AF:

0.757

AC:

11561

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.866

AC:

3004

AN:

3470

East Asian (EAS)

AF:

0.713

AC:

3674

AN:

5156

South Asian (SAS)

AF:

0.783

AC:

3766

AN:

4808

European-Finnish (FIN)

AF:

0.877

AC:

9288

AN:

10596

Middle Eastern (MID)

AF:

0.915

AC:

269

AN:

294

European-Non Finnish (NFE)

AF:

0.810

AC:

55084

AN:

67970

Other (OTH)

AF:

0.857

AC:

1803

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

968

1936

2903

3871

4839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

884

1768

2652

3536

4420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.822

Hom.:

119060

Bravo

AF:

0.847

Asia WGS

AF:

0.766

AC:

2661

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.9

(source)

DANN

Benign

0.62

PhyloP100

-0.23

PromoterAI

-0.038

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over