chr15-84887913-G-A

Variant summary

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

The NM_004213.5(SLC28A1):​c.96+57G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,289,002 control chromosomes in the GnomAD database, including 28,445 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 0.17 ( 2703 hom., cov: 32)
Exomes 𝑓: 0.21 ( 25742 hom. )

Consequence

SLC28A1
NM_004213.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918

Publications

8 publications found
Variant links:
Genes affected
SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC28A1NM_004213.5 linkc.96+57G>A intron_variant Intron 3 of 18 ENST00000394573.6 NP_004204.3 O00337-1B7Z3L5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC28A1ENST00000394573.6 linkc.96+57G>A intron_variant Intron 3 of 18 1 NM_004213.5 ENSP00000378074.1 O00337-1
SLC28A1ENST00000286749.3 linkc.96+57G>A intron_variant Intron 2 of 17 1 ENSP00000286749.3 O00337-1
SLC28A1ENST00000338602.6 linkc.96+57G>A intron_variant Intron 3 of 6 1 ENSP00000341629.2 O00337-2
SLC28A1ENST00000538177.5 linkc.96+57G>A intron_variant Intron 2 of 14 2 ENSP00000443752.1 B7Z3L6

Frequencies

GnomAD3 genomes
AF:
0.167
AC:
25313
AN:
151974
Hom.:
2706
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0398
Gnomad AMI
AF:
0.221
Gnomad AMR
AF:
0.198
Gnomad ASJ
AF:
0.231
Gnomad EAS
AF:
0.119
Gnomad SAS
AF:
0.125
Gnomad FIN
AF:
0.254
Gnomad MID
AF:
0.204
Gnomad NFE
AF:
0.225
Gnomad OTH
AF:
0.183
GnomAD4 exome
AF:
0.208
AC:
236763
AN:
1136910
Hom.:
25742
AF XY:
0.208
AC XY:
120923
AN XY:
581458
show subpopulations
African (AFR)
AF:
0.0336
AC:
905
AN:
26944
American (AMR)
AF:
0.199
AC:
8769
AN:
44150
Ashkenazi Jewish (ASJ)
AF:
0.235
AC:
5641
AN:
24024
East Asian (EAS)
AF:
0.114
AC:
4356
AN:
38262
South Asian (SAS)
AF:
0.142
AC:
11285
AN:
79610
European-Finnish (FIN)
AF:
0.250
AC:
13277
AN:
53206
Middle Eastern (MID)
AF:
0.250
AC:
1267
AN:
5066
European-Non Finnish (NFE)
AF:
0.222
AC:
181546
AN:
816024
Other (OTH)
AF:
0.196
AC:
9717
AN:
49624
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
9687
19374
29060
38747
48434
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
5260
10520
15780
21040
26300
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.166
AC:
25300
AN:
152092
Hom.:
2703
Cov.:
32
AF XY:
0.166
AC XY:
12358
AN XY:
74336
show subpopulations
African (AFR)
AF:
0.0398
AC:
1651
AN:
41530
American (AMR)
AF:
0.197
AC:
3017
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.231
AC:
800
AN:
3468
East Asian (EAS)
AF:
0.118
AC:
611
AN:
5164
South Asian (SAS)
AF:
0.124
AC:
600
AN:
4820
European-Finnish (FIN)
AF:
0.254
AC:
2683
AN:
10562
Middle Eastern (MID)
AF:
0.195
AC:
57
AN:
292
European-Non Finnish (NFE)
AF:
0.225
AC:
15296
AN:
67948
Other (OTH)
AF:
0.181
AC:
383
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1044
2089
3133
4178
5222
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
270
540
810
1080
1350
<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:
0.203
Hom.:
9549
Bravo
AF:
0.158
Asia WGS
AF:
0.115
AC:
398
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.45
DANN
Benign
0.38
PhyloP100
-0.92
Mutation Taster
=100/0
polymorphism (auto)

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: rs12442557; hg19: chr15-85431144; COSMIC: COSV54476333; API