GeneBe

1-175192463-G-T

Variant names:

Variant summary

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

The NM_014656.3(KIAA0040):​c.-384+177C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,018 control chromosomes in the GnomAD database, including 5,487 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 0.24 ( 5487 hom., cov: 32)

Consequence

KIAA0040
NM_014656.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131

Publications

9 publications found
Variant links:
Genes affected
KIAA0040 (HGNC:28950): (KIAA0040) Predicted to be integral component of 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=-0.75).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIAA0040NM_014656.3 linkc.-384+177C>A intron_variant Intron 1 of 3 ENST00000423313.6 NP_055471.2 Q15053

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIAA0040ENST00000423313.6 linkc.-384+177C>A intron_variant Intron 1 of 3 1 NM_014656.3 ENSP00000462172.1 Q15053

Frequencies

GnomAD3 genomes
AF:
0.239
AC:
36300
AN:
151900
Hom.:
5476
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0709
Gnomad AMI
AF:
0.424
Gnomad AMR
AF:
0.442
Gnomad ASJ
AF:
0.340
Gnomad EAS
AF:
0.344
Gnomad SAS
AF:
0.306
Gnomad FIN
AF:
0.195
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.281
Gnomad OTH
AF:
0.284
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.239
AC:
36326
AN:
152018
Hom.:
5487
Cov.:
32
AF XY:
0.241
AC XY:
17883
AN XY:
74292
show subpopulations
African (AFR)
AF:
0.0709
AC:
2941
AN:
41510
American (AMR)
AF:
0.442
AC:
6750
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.340
AC:
1178
AN:
3464
East Asian (EAS)
AF:
0.345
AC:
1773
AN:
5138
South Asian (SAS)
AF:
0.306
AC:
1469
AN:
4804
European-Finnish (FIN)
AF:
0.195
AC:
2056
AN:
10564
Middle Eastern (MID)
AF:
0.293
AC:
86
AN:
294
European-Non Finnish (NFE)
AF:
0.281
AC:
19085
AN:
67958
Other (OTH)
AF:
0.285
AC:
603
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1277
2554
3830
5107
6384
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
384
768
1152
1536
1920
<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:
0.204
Hom.:
909
Bravo
AF:
0.255
Asia WGS
AF:
0.315
AC:
1094
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
8.1
DANN
Benign
0.85
PhyloP100
0.13
PromoterAI
-0.036
Neutral
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: rs2272785; hg19: chr1-175161599; API