ENST00000413541.1:n.965-158C>A

Variant summary

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

The ENST00000413541.1(SLC44A3-AS1):​n.965-158C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,030 control chromosomes in the GnomAD database, including 4,911 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 0.24 ( 4911 hom., cov: 33)

Consequence

SLC44A3-AS1
ENST00000413541.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.14

Publications

14 publications found
Variant links:
Genes affected

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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105378861XR_001738160.3 linkn.511+23307G>T intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC44A3-AS1ENST00000413541.1 linkn.965-158C>A intron_variant Intron 1 of 1 2
SLC44A3-AS1ENST00000414374.2 linkn.439-158C>A intron_variant Intron 2 of 2 3
ENSG00000301906ENST00000782778.1 linkn.341+23307G>T intron_variant Intron 1 of 2
ENSG00000301906ENST00000782779.1 linkn.331-8486G>T intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.236
AC:
35839
AN:
151910
Hom.:
4916
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.269
Gnomad ASJ
AF:
0.432
Gnomad EAS
AF:
0.257
Gnomad SAS
AF:
0.245
Gnomad FIN
AF:
0.252
Gnomad MID
AF:
0.271
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.236
AC:
35838
AN:
152030
Hom.:
4911
Cov.:
33
AF XY:
0.235
AC XY:
17491
AN XY:
74314
show subpopulations
African (AFR)
AF:
0.101
AC:
4183
AN:
41482
American (AMR)
AF:
0.269
AC:
4106
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.432
AC:
1497
AN:
3468
East Asian (EAS)
AF:
0.257
AC:
1332
AN:
5174
South Asian (SAS)
AF:
0.245
AC:
1182
AN:
4816
European-Finnish (FIN)
AF:
0.252
AC:
2659
AN:
10560
Middle Eastern (MID)
AF:
0.276
AC:
81
AN:
294
European-Non Finnish (NFE)
AF:
0.294
AC:
20008
AN:
67942
Other (OTH)
AF:
0.256
AC:
540
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1359
2717
4076
5434
6793
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
378
756
1134
1512
1890
<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:
0.277
Hom.:
19678
Bravo
AF:
0.231
Asia WGS
AF:
0.246
AC:
855
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
13
DANN
Benign
0.42
PhyloP100
2.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs2022309; hg19: chr1-95052476; API