chr19-49971760-G-A

Variant summary

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

The ENST00000602139.6(SIGLEC16):​c.1017+46G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,607,248 control chromosomes in the GnomAD database, including 29,475 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 0.18 ( 3009 hom., cov: 30)
Exomes 𝑓: 0.19 ( 26466 hom. )

Consequence

SIGLEC16
ENST00000602139.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

9 publications found
Variant links:
Genes affected
SIGLEC16 (HGNC:24851): (sialic acid binding Ig like lectin 16) Predicted to enable sialic acid binding activity. Involved in positive regulation of defense response to bacterium and positive regulation of interleukin-6 production. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SIGLEC16NM_001348364.2 linkc.1015+46G>A intron_variant Intron 6 of 9 NP_001335293.2
SIGLEC16NR_145574.2 linkn.1055+46G>A intron_variant Intron 5 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SIGLEC16ENST00000602139.6 linkc.1017+46G>A intron_variant Intron 5 of 8 5 ENSP00000502223.2
ENSG00000301908ENST00000782794.1 linkn.158+283C>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27333
AN:
151484
Hom.:
3005
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.151
Gnomad AMI
AF:
0.337
Gnomad AMR
AF:
0.151
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.325
Gnomad SAS
AF:
0.142
Gnomad FIN
AF:
0.134
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.199
Gnomad OTH
AF:
0.191
GnomAD2 exomes
AF:
0.185
AC:
46388
AN:
250160
AF XY:
0.186
show subpopulations
Gnomad AFR exome
AF:
0.149
Gnomad AMR exome
AF:
0.137
Gnomad ASJ exome
AF:
0.218
Gnomad EAS exome
AF:
0.320
Gnomad FIN exome
AF:
0.145
Gnomad NFE exome
AF:
0.198
Gnomad OTH exome
AF:
0.193
GnomAD4 exome
AF:
0.185
AC:
269671
AN:
1455646
Hom.:
26466
Cov.:
40
AF XY:
0.185
AC XY:
134200
AN XY:
724258
show subpopulations
African (AFR)
AF:
0.151
AC:
5052
AN:
33406
American (AMR)
AF:
0.139
AC:
6219
AN:
44642
Ashkenazi Jewish (ASJ)
AF:
0.219
AC:
5698
AN:
25998
East Asian (EAS)
AF:
0.323
AC:
12799
AN:
39670
South Asian (SAS)
AF:
0.156
AC:
13474
AN:
86132
European-Finnish (FIN)
AF:
0.148
AC:
7867
AN:
53316
Middle Eastern (MID)
AF:
0.266
AC:
1511
AN:
5690
European-Non Finnish (NFE)
AF:
0.186
AC:
205561
AN:
1106666
Other (OTH)
AF:
0.191
AC:
11490
AN:
60126
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.459
Heterozygous variant carriers
0
12181
24362
36544
48725
60906
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
7118
14236
21354
28472
35590
<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:
0.180
AC:
27353
AN:
151602
Hom.:
3009
Cov.:
30
AF XY:
0.179
AC XY:
13229
AN XY:
74076
show subpopulations
African (AFR)
AF:
0.151
AC:
6253
AN:
41440
American (AMR)
AF:
0.150
AC:
2287
AN:
15212
Ashkenazi Jewish (ASJ)
AF:
0.220
AC:
760
AN:
3450
East Asian (EAS)
AF:
0.326
AC:
1679
AN:
5156
South Asian (SAS)
AF:
0.142
AC:
682
AN:
4808
European-Finnish (FIN)
AF:
0.134
AC:
1413
AN:
10558
Middle Eastern (MID)
AF:
0.238
AC:
70
AN:
294
European-Non Finnish (NFE)
AF:
0.199
AC:
13501
AN:
67676
Other (OTH)
AF:
0.191
AC:
401
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
1072
2144
3215
4287
5359
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
290
580
870
1160
1450
<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:
0.203
Hom.:
679
Bravo
AF:
0.183
Asia WGS
AF:
0.204
AC:
709
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.2
DANN
Benign
0.50
PhyloP100
-1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs12462972; hg19: chr19-50475017; COSMIC: COSV57465026; API