GeneBe

NM_019590.5:c.354+36221A>T

Variant names:

Variant summary

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

The NM_019590.5(KIAA1217):​c.354+36221A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 150,686 control chromosomes in the GnomAD database, including 39,998 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 0.73 ( 39998 hom., cov: 27)

Consequence

KIAA1217
NM_019590.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.360

Publications

2 publications found
Variant links:
Genes affected
KIAA1217 (HGNC:25428): (KIAA1217) Predicted to be involved in embryonic skeletal system development. Predicted to be active in cytoplasm. [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=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIAA1217NM_019590.5 linkc.354+36221A>T intron_variant Intron 2 of 20 ENST00000376454.8 NP_062536.2 Q5T5P2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIAA1217ENST00000376454.8 linkc.354+36221A>T intron_variant Intron 2 of 20 1 NM_019590.5 ENSP00000365637.3 Q5T5P2-1

Frequencies

GnomAD3 genomes
AF:
0.727
AC:
109427
AN:
150576
Hom.:
39973
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.704
Gnomad AMI
AF:
0.677
Gnomad AMR
AF:
0.792
Gnomad ASJ
AF:
0.781
Gnomad EAS
AF:
0.612
Gnomad SAS
AF:
0.530
Gnomad FIN
AF:
0.773
Gnomad MID
AF:
0.673
Gnomad NFE
AF:
0.740
Gnomad OTH
AF:
0.715
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.727
AC:
109498
AN:
150686
Hom.:
39998
Cov.:
27
AF XY:
0.726
AC XY:
53290
AN XY:
73438
show subpopulations
African (AFR)
AF:
0.704
AC:
28868
AN:
40978
American (AMR)
AF:
0.792
AC:
11924
AN:
15060
Ashkenazi Jewish (ASJ)
AF:
0.781
AC:
2709
AN:
3468
East Asian (EAS)
AF:
0.612
AC:
3091
AN:
5052
South Asian (SAS)
AF:
0.530
AC:
2535
AN:
4782
European-Finnish (FIN)
AF:
0.773
AC:
7841
AN:
10138
Middle Eastern (MID)
AF:
0.672
AC:
195
AN:
290
European-Non Finnish (NFE)
AF:
0.740
AC:
50227
AN:
67908
Other (OTH)
AF:
0.711
AC:
1491
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1472
2944
4417
5889
7361
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
832
1664
2496
3328
4160
<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:
0.749
Hom.:
5321
Bravo
AF:
0.729
Asia WGS
AF:
0.608
AC:
2115
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.70
DANN
Benign
0.80
PhyloP100
-0.36
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs2280172; hg19: chr10-24545059; API