chr2-167059536-G-A

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632

Publications

3 publications found
Variant links:
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
XIRP2NM_152381.6 linkc.409-76373G>A intron_variant Intron 2 of 10 ENST00000409195.6 NP_689594.4 A4UGR9-8
XIRP2NM_001199143.2 linkc.409-76373G>A intron_variant Intron 2 of 10 NP_001186072.1 A4UGR9-6
XIRP2NM_001079810.4 linkc.409-76373G>A intron_variant Intron 2 of 9 NP_001073278.1 A4UGR9-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
XIRP2ENST00000409195.6 linkc.409-76373G>A intron_variant Intron 2 of 10 5 NM_152381.6 ENSP00000386840.2 A4UGR9-8
XIRP2ENST00000409728.5 linkc.409-76373G>A intron_variant Intron 2 of 10 1 ENSP00000386619.1 A4UGR9-6
XIRP2ENST00000409043.5 linkc.409-76373G>A intron_variant Intron 2 of 9 1 ENSP00000386454.1 A4UGR9-4
XIRP2ENST00000672716.1 linkc.433-76373G>A intron_variant Intron 2 of 9 ENSP00000500725.1 A0A5F9ZHW6

Frequencies

GnomAD3 genomes
AF:
0.336
AC:
51029
AN:
151716
Hom.:
10170
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.551
Gnomad AMI
AF:
0.332
Gnomad AMR
AF:
0.252
Gnomad ASJ
AF:
0.344
Gnomad EAS
AF:
0.349
Gnomad SAS
AF:
0.453
Gnomad FIN
AF:
0.154
Gnomad MID
AF:
0.436
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.337
AC:
51116
AN:
151836
Hom.:
10205
Cov.:
32
AF XY:
0.333
AC XY:
24723
AN XY:
74234
show subpopulations
African (AFR)
AF:
0.552
AC:
22808
AN:
41338
American (AMR)
AF:
0.252
AC:
3842
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.344
AC:
1195
AN:
3470
East Asian (EAS)
AF:
0.349
AC:
1799
AN:
5160
South Asian (SAS)
AF:
0.452
AC:
2177
AN:
4820
European-Finnish (FIN)
AF:
0.154
AC:
1620
AN:
10542
Middle Eastern (MID)
AF:
0.442
AC:
129
AN:
292
European-Non Finnish (NFE)
AF:
0.244
AC:
16562
AN:
67930
Other (OTH)
AF:
0.322
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
70-75
75-80
>80
Age
Alfa
AF:
0.287
Hom.:
1779
Bravo
AF:
0.350
Asia WGS
AF:
0.427
AC:
1484
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.55
DANN
Benign
0.61
PhyloP100
-0.63
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: rs3914147; hg19: chr2-167916046; API