chrX-79363537-G-C
Position:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004867.5(ITM2A):āc.129C>Gā(p.Thr43=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,178,363 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 82 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00012 ( 0 hom., 6 hem., cov: 22)
Exomes š: 0.00021 ( 0 hom. 76 hem. )
Consequence
ITM2A
NM_004867.5 synonymous
NM_004867.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.287
Genes affected
ITM2A (HGNC:6173): (integral membrane protein 2A) This gene encodes a type II membrane protein that belongs to the ITM2 family. Studies in mouse suggest that it may be involved in osteo- and chondrogenic differentiation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant X-79363537-G-C is Benign according to our data. Variant chrX-79363537-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2660976.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.287 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITM2A | NM_004867.5 | c.129C>G | p.Thr43= | synonymous_variant | 2/6 | ENST00000373298.7 | |
ITM2A | NM_001171581.2 | c.112-398C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITM2A | ENST00000373298.7 | c.129C>G | p.Thr43= | synonymous_variant | 2/6 | 1 | NM_004867.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000117 AC: 13AN: 110758Hom.: 0 Cov.: 22 AF XY: 0.000182 AC XY: 6AN XY: 33030
GnomAD3 genomes
AF:
AC:
13
AN:
110758
Hom.:
Cov.:
22
AF XY:
AC XY:
6
AN XY:
33030
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:
GnomAD3 exomes AF: 0.0000595 AC: 10AN: 168108Hom.: 0 AF XY: 0.0000360 AC XY: 2AN XY: 55542
GnomAD3 exomes
AF:
AC:
10
AN:
168108
Hom.:
AF XY:
AC XY:
2
AN XY:
55542
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000211 AC: 225AN: 1067605Hom.: 0 Cov.: 27 AF XY: 0.000223 AC XY: 76AN XY: 341529
GnomAD4 exome
AF:
AC:
225
AN:
1067605
Hom.:
Cov.:
27
AF XY:
AC XY:
76
AN XY:
341529
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000117 AC: 13AN: 110758Hom.: 0 Cov.: 22 AF XY: 0.000182 AC XY: 6AN XY: 33030
GnomAD4 genome
AF:
AC:
13
AN:
110758
Hom.:
Cov.:
22
AF XY:
AC XY:
6
AN XY:
33030
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | ITM2A: BP4, BP7, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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