NM_152381.6:c.409-76373G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152381.6(XIRP2):c.409-76373G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,836 control chromosomes in the GnomAD database, including 10,205 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 0.34 ( 10205 hom., cov: 32)
Consequence
XIRP2
NM_152381.6 intron
NM_152381.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.632
Publications
3 publications found
Genes affected
XIRP2 (HGNC:14303): (xin actin binding repeat containing 2) Enables actin filament binding activity. Predicted to be involved in actin cytoskeleton organization and heart development. Predicted to act upstream of or within cardiac muscle tissue morphogenesis; cell-cell junction organization; and ventricular septum development. Colocalizes with focal adhesion and stress fiber. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XIRP2 | NM_152381.6 | c.409-76373G>A | intron_variant | Intron 2 of 10 | ENST00000409195.6 | NP_689594.4 | ||
XIRP2 | NM_001199143.2 | c.409-76373G>A | intron_variant | Intron 2 of 10 | NP_001186072.1 | |||
XIRP2 | NM_001079810.4 | c.409-76373G>A | intron_variant | Intron 2 of 9 | NP_001073278.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XIRP2 | ENST00000409195.6 | c.409-76373G>A | intron_variant | Intron 2 of 10 | 5 | NM_152381.6 | ENSP00000386840.2 | |||
XIRP2 | ENST00000409728.5 | c.409-76373G>A | intron_variant | Intron 2 of 10 | 1 | ENSP00000386619.1 | ||||
XIRP2 | ENST00000409043.5 | c.409-76373G>A | intron_variant | Intron 2 of 9 | 1 | ENSP00000386454.1 | ||||
XIRP2 | ENST00000672716.1 | c.433-76373G>A | intron_variant | Intron 2 of 9 | ENSP00000500725.1 |
Frequencies
GnomAD3 genomes AF: 0.336 AC: 51029AN: 151716Hom.: 10170 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
51029
AN:
151716
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.337 AC: 51116AN: 151836Hom.: 10205 Cov.: 32 AF XY: 0.333 AC XY: 24723AN XY: 74234 show subpopulations
GnomAD4 genome
AF:
AC:
51116
AN:
151836
Hom.:
Cov.:
32
AF XY:
AC XY:
24723
AN XY:
74234
show subpopulations
African (AFR)
AF:
AC:
22808
AN:
41338
American (AMR)
AF:
AC:
3842
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
AC:
1195
AN:
3470
East Asian (EAS)
AF:
AC:
1799
AN:
5160
South Asian (SAS)
AF:
AC:
2177
AN:
4820
European-Finnish (FIN)
AF:
AC:
1620
AN:
10542
Middle Eastern (MID)
AF:
AC:
129
AN:
292
European-Non Finnish (NFE)
AF:
AC:
16562
AN:
67930
Other (OTH)
AF:
AC:
681
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.493
Heterozygous variant carriers
0
1523
3046
4568
6091
7614
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
500
1000
1500
2000
2500
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1484
AN:
3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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