GeneBe

17-27754003-C-G

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 0.25 in 1,482,516 control chromosomes in the GnomAD database, including 47,530 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 ( 4471 hom., cov: 32)
Exomes 𝑓: 0.25 ( 43059 hom. )

Consequence

LGALS9DP
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.726

Publications

8 publications found
Variant links:
Genes affected
LGALS9DP (HGNC:49896): (galectin 9D, pseudogene)

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 (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LGALS9DP n.27754003C>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LGALS9DPENST00000580112.1 linkn.516-83C>G intron_variant Intron 5 of 7 6

Frequencies

GnomAD3 genomes
AF:
0.240
AC:
36471
AN:
152022
Hom.:
4472
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.230
Gnomad AMR
AF:
0.312
Gnomad ASJ
AF:
0.256
Gnomad EAS
AF:
0.238
Gnomad SAS
AF:
0.341
Gnomad FIN
AF:
0.208
Gnomad MID
AF:
0.263
Gnomad NFE
AF:
0.241
Gnomad OTH
AF:
0.267
GnomAD4 exome
AF:
0.251
AC:
334252
AN:
1330378
Hom.:
43059
AF XY:
0.254
AC XY:
169863
AN XY:
668298
show subpopulations
African (AFR)
AF:
0.206
AC:
6385
AN:
30954
American (AMR)
AF:
0.327
AC:
14451
AN:
44218
Ashkenazi Jewish (ASJ)
AF:
0.263
AC:
6640
AN:
25260
East Asian (EAS)
AF:
0.291
AC:
11283
AN:
38796
South Asian (SAS)
AF:
0.342
AC:
28597
AN:
83532
European-Finnish (FIN)
AF:
0.209
AC:
10961
AN:
52354
Middle Eastern (MID)
AF:
0.278
AC:
1074
AN:
3862
European-Non Finnish (NFE)
AF:
0.242
AC:
240776
AN:
995926
Other (OTH)
AF:
0.254
AC:
14085
AN:
55476
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
12912
25824
38737
51649
64561
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
8000
16000
24000
32000
40000
<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:
0.240
AC:
36493
AN:
152138
Hom.:
4471
Cov.:
32
AF XY:
0.240
AC XY:
17832
AN XY:
74394
show subpopulations
African (AFR)
AF:
0.205
AC:
8517
AN:
41518
American (AMR)
AF:
0.312
AC:
4767
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.256
AC:
887
AN:
3468
East Asian (EAS)
AF:
0.238
AC:
1230
AN:
5170
South Asian (SAS)
AF:
0.340
AC:
1638
AN:
4820
European-Finnish (FIN)
AF:
0.208
AC:
2205
AN:
10590
Middle Eastern (MID)
AF:
0.265
AC:
78
AN:
294
European-Non Finnish (NFE)
AF:
0.241
AC:
16404
AN:
67970
Other (OTH)
AF:
0.264
AC:
557
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1445
2890
4336
5781
7226
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:
0.123
Hom.:
190
Bravo
AF:
0.244
Asia WGS
AF:
0.278
AC:
966
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.3
DANN
Benign
0.65
PhyloP100
-0.73

Splicing

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

Publications

Other links and lift over

dbSNP: rs9901734; hg19: chr17-26081029; COSMIC: COSV58224149; API