GeneBe

chr17-27747965-A-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 0.451 in 364,054 control chromosomes in the GnomAD database, including 37,780 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 0.47 ( 16823 hom., cov: 32)
Exomes 𝑓: 0.44 ( 20957 hom. )

Consequence

LGALS9DP
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0450

Publications

12 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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LGALS9DP n.27747965A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LGALS9DPENST00000580112.1 linkn.93-139A>G intron_variant Intron 1 of 7 6

Frequencies

GnomAD3 genomes
AF:
0.467
AC:
70928
AN:
151988
Hom.:
16809
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.524
Gnomad AMI
AF:
0.605
Gnomad AMR
AF:
0.500
Gnomad ASJ
AF:
0.445
Gnomad EAS
AF:
0.487
Gnomad SAS
AF:
0.462
Gnomad FIN
AF:
0.410
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.430
Gnomad OTH
AF:
0.499
GnomAD4 exome
AF:
0.440
AC:
93230
AN:
211948
Hom.:
20957
AF XY:
0.443
AC XY:
52007
AN XY:
117348
show subpopulations
African (AFR)
AF:
0.524
AC:
2579
AN:
4924
American (AMR)
AF:
0.474
AC:
4534
AN:
9560
Ashkenazi Jewish (ASJ)
AF:
0.467
AC:
2038
AN:
4366
East Asian (EAS)
AF:
0.494
AC:
3673
AN:
7432
South Asian (SAS)
AF:
0.471
AC:
18934
AN:
40178
European-Finnish (FIN)
AF:
0.398
AC:
9336
AN:
23452
Middle Eastern (MID)
AF:
0.512
AC:
348
AN:
680
European-Non Finnish (NFE)
AF:
0.426
AC:
47562
AN:
111728
Other (OTH)
AF:
0.439
AC:
4226
AN:
9628
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
2445
4889
7334
9778
12223
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
322
644
966
1288
1610
<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:
0.467
AC:
70976
AN:
152106
Hom.:
16823
Cov.:
32
AF XY:
0.466
AC XY:
34653
AN XY:
74344
show subpopulations
African (AFR)
AF:
0.524
AC:
21759
AN:
41494
American (AMR)
AF:
0.500
AC:
7638
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.445
AC:
1544
AN:
3472
East Asian (EAS)
AF:
0.486
AC:
2515
AN:
5172
South Asian (SAS)
AF:
0.462
AC:
2225
AN:
4818
European-Finnish (FIN)
AF:
0.410
AC:
4324
AN:
10554
Middle Eastern (MID)
AF:
0.524
AC:
153
AN:
292
European-Non Finnish (NFE)
AF:
0.430
AC:
29225
AN:
67994
Other (OTH)
AF:
0.492
AC:
1041
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1978
3957
5935
7914
9892
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
646
1292
1938
2584
3230
<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:
0.448
Hom.:
2715
Bravo
AF:
0.476
Asia WGS
AF:
0.447
AC:
1556
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.2
DANN
Benign
0.70
PhyloP100
0.045

Splicing

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

Publications

Other links and lift over

dbSNP: rs4796017; hg19: chr17-26074991; API