GeneBe

16-55655175-C-G

Variant names:

Variant summary

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

The XR_007065075.1(LOC124903693):​n.515+424G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,080 control chromosomes in the GnomAD database, including 29,318 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 0.62 ( 29318 hom., cov: 32)

Consequence

LOC124903693
XR_007065075.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.327

Publications

8 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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124903693XR_007065075.1 linkn.515+424G>C intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.620
AC:
94183
AN:
151962
Hom.:
29293
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.649
Gnomad AMI
AF:
0.586
Gnomad AMR
AF:
0.647
Gnomad ASJ
AF:
0.598
Gnomad EAS
AF:
0.685
Gnomad SAS
AF:
0.702
Gnomad FIN
AF:
0.561
Gnomad MID
AF:
0.579
Gnomad NFE
AF:
0.596
Gnomad OTH
AF:
0.620
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.620
AC:
94266
AN:
152080
Hom.:
29318
Cov.:
32
AF XY:
0.623
AC XY:
46278
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.649
AC:
26925
AN:
41486
American (AMR)
AF:
0.647
AC:
9891
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.598
AC:
2076
AN:
3472
East Asian (EAS)
AF:
0.684
AC:
3531
AN:
5162
South Asian (SAS)
AF:
0.702
AC:
3377
AN:
4808
European-Finnish (FIN)
AF:
0.561
AC:
5936
AN:
10578
Middle Eastern (MID)
AF:
0.585
AC:
172
AN:
294
European-Non Finnish (NFE)
AF:
0.596
AC:
40507
AN:
67976
Other (OTH)
AF:
0.625
AC:
1317
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1849
3698
5548
7397
9246
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
780
1560
2340
3120
3900
<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:
0.471
Hom.:
1124
Bravo
AF:
0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.1
DANN
Benign
0.37
PhyloP100
-0.33

Splicing

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

Publications

Other links and lift over

dbSNP: rs2397771; hg19: chr16-55689087; API