GeneBe

14-106684476-T-C

Variant names:

Variant summary

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

The variant allele was found at a frequency of 0.246 in 151,994 control chromosomes in the GnomAD database, including 5,060 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 0.25 ( 5060 hom., cov: 33)
Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

IGH
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

7 publications found
Variant links:
Genes affected
SLC20A1P1 (HGNC:20051): (solute carrier family 20 member 1 pseudogene 1)

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=-0.67).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IGH n.106684476T>C intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC20A1P1ENST00000413906.2 linkn.-126A>G upstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.246
AC:
37306
AN:
151880
Hom.:
5056
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.163
Gnomad AMI
AF:
0.221
Gnomad AMR
AF:
0.247
Gnomad ASJ
AF:
0.335
Gnomad EAS
AF:
0.345
Gnomad SAS
AF:
0.493
Gnomad FIN
AF:
0.271
Gnomad MID
AF:
0.353
Gnomad NFE
AF:
0.262
Gnomad OTH
AF:
0.263
GnomAD4 exome
AF:
0.500
AC:
1
AN:
2
Hom.:
0
AC XY:
0
AN XY:
0
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.500
AC:
1
AN:
2
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.246
AC:
37326
AN:
151992
Hom.:
5060
Cov.:
33
AF XY:
0.250
AC XY:
18594
AN XY:
74296
show subpopulations
African (AFR)
AF:
0.163
AC:
6741
AN:
41432
American (AMR)
AF:
0.247
AC:
3778
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.335
AC:
1163
AN:
3468
East Asian (EAS)
AF:
0.346
AC:
1779
AN:
5138
South Asian (SAS)
AF:
0.492
AC:
2366
AN:
4808
European-Finnish (FIN)
AF:
0.271
AC:
2866
AN:
10582
Middle Eastern (MID)
AF:
0.348
AC:
101
AN:
290
European-Non Finnish (NFE)
AF:
0.262
AC:
17780
AN:
67978
Other (OTH)
AF:
0.261
AC:
550
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1433
2866
4300
5733
7166
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
412
824
1236
1648
2060
<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:
0.197
Hom.:
729
Bravo
AF:
0.238
Asia WGS
AF:
0.387
AC:
1346
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
0.48
DANN
Benign
0.38
PhyloP100
-1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs17113284; hg19: chr14-107140493; API