chr22-43972324-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_015380.5(SAMM50):ā€‹c.411A>Gā€‹(p.Gly137=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 1,588,460 control chromosomes in the GnomAD database, including 230,729 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.58 ( 26765 hom., cov: 32)
Exomes š‘“: 0.53 ( 203964 hom. )

Consequence

SAMM50
NM_015380.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.553
Variant links:
Genes affected
SAMM50 (HGNC:24276): (SAMM50 sorting and assembly machinery component) This gene encodes a component of the Sorting and Assembly Machinery (SAM) of the mitochondrial outer membrane. The Sam complex functions in the assembly of beta-barrel proteins into the outer mitochondrial membrane.[provided by RefSeq, Jun 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 22-43972324-A-G is Benign according to our data. Variant chr22-43972324-A-G is described in ClinVar as [Benign]. Clinvar id is 1283359.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.553 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SAMM50NM_015380.5 linkuse as main transcriptc.411A>G p.Gly137= synonymous_variant 5/15 ENST00000350028.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SAMM50ENST00000350028.5 linkuse as main transcriptc.411A>G p.Gly137= synonymous_variant 5/151 NM_015380.5 P1
SAMM50ENST00000493161.1 linkuse as main transcriptn.593A>G non_coding_transcript_exon_variant 5/73

Frequencies

GnomAD3 genomes
AF:
0.584
AC:
88798
AN:
151924
Hom.:
26717
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.711
Gnomad AMI
AF:
0.509
Gnomad AMR
AF:
0.529
Gnomad ASJ
AF:
0.464
Gnomad EAS
AF:
0.828
Gnomad SAS
AF:
0.699
Gnomad FIN
AF:
0.608
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.499
Gnomad OTH
AF:
0.525
GnomAD3 exomes
AF:
0.572
AC:
136052
AN:
237666
Hom.:
40437
AF XY:
0.571
AC XY:
73387
AN XY:
128634
show subpopulations
Gnomad AFR exome
AF:
0.716
Gnomad AMR exome
AF:
0.538
Gnomad ASJ exome
AF:
0.450
Gnomad EAS exome
AF:
0.829
Gnomad SAS exome
AF:
0.690
Gnomad FIN exome
AF:
0.603
Gnomad NFE exome
AF:
0.500
Gnomad OTH exome
AF:
0.521
GnomAD4 exome
AF:
0.526
AC:
755054
AN:
1436420
Hom.:
203964
Cov.:
27
AF XY:
0.530
AC XY:
378519
AN XY:
714690
show subpopulations
Gnomad4 AFR exome
AF:
0.713
Gnomad4 AMR exome
AF:
0.535
Gnomad4 ASJ exome
AF:
0.447
Gnomad4 EAS exome
AF:
0.850
Gnomad4 SAS exome
AF:
0.685
Gnomad4 FIN exome
AF:
0.610
Gnomad4 NFE exome
AF:
0.494
Gnomad4 OTH exome
AF:
0.537
GnomAD4 genome
AF:
0.585
AC:
88897
AN:
152040
Hom.:
26765
Cov.:
32
AF XY:
0.590
AC XY:
43856
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.711
Gnomad4 AMR
AF:
0.530
Gnomad4 ASJ
AF:
0.464
Gnomad4 EAS
AF:
0.827
Gnomad4 SAS
AF:
0.697
Gnomad4 FIN
AF:
0.608
Gnomad4 NFE
AF:
0.499
Gnomad4 OTH
AF:
0.531
Alfa
AF:
0.515
Hom.:
47673
Bravo
AF:
0.584
Asia WGS
AF:
0.758
AC:
2637
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxMar 26, 2021- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
CADD
Benign
5.1
DANN
Benign
0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3177036; hg19: chr22-44368204; COSMIC: COSV63109448; COSMIC: COSV63109448; API