chr5-16444840-A-G

Variant summary

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

The ENST00000773338.1(ENSG00000300672):​n.429+2551A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,140 control chromosomes in the GnomAD database, including 33,632 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 0.66 ( 33632 hom., cov: 33)

Consequence

ENSG00000300672
ENST00000773338.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.238

Publications

5 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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000300672ENST00000773338.1 linkn.429+2551A>G intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.663
AC:
100792
AN:
152020
Hom.:
33608
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.622
Gnomad AMI
AF:
0.581
Gnomad AMR
AF:
0.657
Gnomad ASJ
AF:
0.686
Gnomad EAS
AF:
0.468
Gnomad SAS
AF:
0.542
Gnomad FIN
AF:
0.760
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.698
Gnomad OTH
AF:
0.661
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.663
AC:
100878
AN:
152140
Hom.:
33632
Cov.:
33
AF XY:
0.662
AC XY:
49237
AN XY:
74396
show subpopulations
African (AFR)
AF:
0.622
AC:
25790
AN:
41488
American (AMR)
AF:
0.657
AC:
10046
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.686
AC:
2382
AN:
3472
East Asian (EAS)
AF:
0.467
AC:
2416
AN:
5168
South Asian (SAS)
AF:
0.544
AC:
2622
AN:
4816
European-Finnish (FIN)
AF:
0.760
AC:
8048
AN:
10594
Middle Eastern (MID)
AF:
0.650
AC:
191
AN:
294
European-Non Finnish (NFE)
AF:
0.698
AC:
47456
AN:
68000
Other (OTH)
AF:
0.664
AC:
1402
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1748
3496
5245
6993
8741
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
800
1600
2400
3200
4000
<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:
0.685
Hom.:
17024
Bravo
AF:
0.655
Asia WGS
AF:
0.538
AC:
1866
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.22
DANN
Benign
0.51
PhyloP100
-0.24

Splicing

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

Publications

Other links and lift over

dbSNP: rs162859; hg19: chr5-16444949; API