GeneBe

6-129942446-T-C

Variant names:

Variant summary

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

The XR_942986.3(LOC105377999):​n.778+4422T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,118 control chromosomes in the GnomAD database, including 4,136 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 0.23 ( 4136 hom., cov: 32)

Consequence

LOC105377999
XR_942986.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.454

Publications

4 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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105377999XR_942986.3 linkn.778+4422T>C intron_variant Intron 7 of 7

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.225
AC:
34242
AN:
152000
Hom.:
4120
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.168
Gnomad AMI
AF:
0.270
Gnomad AMR
AF:
0.316
Gnomad ASJ
AF:
0.167
Gnomad EAS
AF:
0.290
Gnomad SAS
AF:
0.239
Gnomad FIN
AF:
0.290
Gnomad MID
AF:
0.204
Gnomad NFE
AF:
0.226
Gnomad OTH
AF:
0.245
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.225
AC:
34273
AN:
152118
Hom.:
4136
Cov.:
32
AF XY:
0.230
AC XY:
17140
AN XY:
74362
show subpopulations
African (AFR)
AF:
0.168
AC:
6979
AN:
41524
American (AMR)
AF:
0.316
AC:
4832
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.167
AC:
580
AN:
3468
East Asian (EAS)
AF:
0.290
AC:
1501
AN:
5174
South Asian (SAS)
AF:
0.241
AC:
1159
AN:
4818
European-Finnish (FIN)
AF:
0.290
AC:
3059
AN:
10558
Middle Eastern (MID)
AF:
0.192
AC:
56
AN:
292
European-Non Finnish (NFE)
AF:
0.226
AC:
15342
AN:
67988
Other (OTH)
AF:
0.246
AC:
519
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1335
2669
4004
5338
6673
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
368
736
1104
1472
1840
<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:
0.227
Hom.:
6747
Bravo
AF:
0.225
Asia WGS
AF:
0.280
AC:
972
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
7.7
DANN
Benign
0.77
PhyloP100
-0.45

Splicing

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

Publications

Other links and lift over

dbSNP: rs9375683; hg19: chr6-130263591; API