GeneBe

ENST00000376462.5:c.-320-65914C>T

Variant names:

Variant summary

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

The ENST00000376462.5(KIAA1217):​c.-320-65914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,076 control chromosomes in the GnomAD database, including 3,320 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 0.20 ( 3320 hom., cov: 32)

Consequence

KIAA1217
ENST00000376462.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0150

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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIAA1217NM_001098500.3 linkc.-320-65914C>T intron_variant Intron 1 of 18 NP_001091970.1 Q5T5P2-9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIAA1217ENST00000376462.5 linkc.-320-65914C>T intron_variant Intron 1 of 18 1 ENSP00000365645.1 Q5T5P2-9

Frequencies

GnomAD3 genomes
AF:
0.200
AC:
30466
AN:
151958
Hom.:
3319
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.142
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.204
Gnomad ASJ
AF:
0.299
Gnomad EAS
AF:
0.0770
Gnomad SAS
AF:
0.204
Gnomad FIN
AF:
0.202
Gnomad MID
AF:
0.280
Gnomad NFE
AF:
0.239
Gnomad OTH
AF:
0.208
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.200
AC:
30482
AN:
152076
Hom.:
3320
Cov.:
32
AF XY:
0.200
AC XY:
14859
AN XY:
74324
show subpopulations
African (AFR)
AF:
0.142
AC:
5915
AN:
41512
American (AMR)
AF:
0.204
AC:
3116
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.299
AC:
1039
AN:
3470
East Asian (EAS)
AF:
0.0773
AC:
400
AN:
5172
South Asian (SAS)
AF:
0.203
AC:
979
AN:
4816
European-Finnish (FIN)
AF:
0.202
AC:
2132
AN:
10540
Middle Eastern (MID)
AF:
0.267
AC:
78
AN:
292
European-Non Finnish (NFE)
AF:
0.239
AC:
16256
AN:
67978
Other (OTH)
AF:
0.208
AC:
439
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1248
2495
3743
4990
6238
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
336
672
1008
1344
1680
<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:
0.239
Hom.:
4974
Bravo
AF:
0.199
Asia WGS
AF:
0.150
AC:
523
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
3.2
DANN
Benign
0.97
PhyloP100
-0.015
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs11013804; hg19: chr10-24230240; API