GeneBe

17-27748474-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 0.509 in 472,502 control chromosomes in the GnomAD database, including 63,544 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 0.56 ( 24777 hom., cov: 32)
Exomes 𝑓: 0.49 ( 38767 hom. )

Consequence

LGALS9DP
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

13 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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LGALS9DP n.27748474T>C intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LGALS9DPENST00000580112.1 linkn.317+146T>C intron_variant Intron 2 of 7 6

Frequencies

GnomAD3 genomes
AF:
0.556
AC:
84402
AN:
151916
Hom.:
24752
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.753
Gnomad AMI
AF:
0.641
Gnomad AMR
AF:
0.568
Gnomad ASJ
AF:
0.474
Gnomad EAS
AF:
0.496
Gnomad SAS
AF:
0.514
Gnomad FIN
AF:
0.471
Gnomad MID
AF:
0.563
Gnomad NFE
AF:
0.456
Gnomad OTH
AF:
0.558
GnomAD4 exome
AF:
0.487
AC:
156180
AN:
320468
Hom.:
38767
AF XY:
0.489
AC XY:
88625
AN XY:
181076
show subpopulations
African (AFR)
AF:
0.753
AC:
6479
AN:
8606
American (AMR)
AF:
0.537
AC:
14629
AN:
27230
Ashkenazi Jewish (ASJ)
AF:
0.482
AC:
5213
AN:
10814
East Asian (EAS)
AF:
0.504
AC:
4853
AN:
9632
South Asian (SAS)
AF:
0.529
AC:
31425
AN:
59412
European-Finnish (FIN)
AF:
0.453
AC:
12488
AN:
27562
Middle Eastern (MID)
AF:
0.549
AC:
849
AN:
1546
European-Non Finnish (NFE)
AF:
0.454
AC:
73147
AN:
161228
Other (OTH)
AF:
0.492
AC:
7097
AN:
14438
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.527
Heterozygous variant carriers
0
4109
8218
12326
16435
20544
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
484
968
1452
1936
2420
<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:
0.556
AC:
84468
AN:
152034
Hom.:
24777
Cov.:
32
AF XY:
0.555
AC XY:
41257
AN XY:
74288
show subpopulations
African (AFR)
AF:
0.752
AC:
31213
AN:
41486
American (AMR)
AF:
0.569
AC:
8686
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.474
AC:
1645
AN:
3468
East Asian (EAS)
AF:
0.496
AC:
2564
AN:
5172
South Asian (SAS)
AF:
0.514
AC:
2477
AN:
4822
European-Finnish (FIN)
AF:
0.471
AC:
4957
AN:
10530
Middle Eastern (MID)
AF:
0.565
AC:
166
AN:
294
European-Non Finnish (NFE)
AF:
0.456
AC:
31013
AN:
67970
Other (OTH)
AF:
0.551
AC:
1164
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1830
3660
5489
7319
9149
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
710
1420
2130
2840
3550
<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:
0.515
Hom.:
2755
Bravo
AF:
0.572
Asia WGS
AF:
0.488
AC:
1700
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.6
DANN
Benign
0.45
PhyloP100
-1.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs7215373; hg19: chr17-26075500; API