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GeneBe

rs2075650

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001128917.2(TOMM40):c.275-31A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151888 control chromosomes in the gnomAD Genomes database, including 1333 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 0.13 ( 1333 hom., cov: 32)
Exomes 𝑓: 0.13 ( 2148 hom. )

Consequence

TOMM40
NM_001128917.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TOMM40NM_001128917.2 linkuse as main transcriptc.275-31A>G intron_variant ENST00000426677.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TOMM40ENST00000426677.7 linkuse as main transcriptc.275-31A>G intron_variant 1 NM_001128917.2 P1O96008-1

Frequencies

GnomAD3 genomes
AF:
0.132
AC:
20043
AN:
151888
Hom.:
1333
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.129
Gnomad AMI
AF:
0.144
Gnomad AMR
AF:
0.105
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.108
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.172
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.138
Gnomad OTH
AF:
0.0970
GnomAD3 exomes
AF:
0.129
AC:
32485
AN:
251370
Hom.:
2148
AF XY:
0.129
AC XY:
17530
AN XY:
135868
show subpopulations
Gnomad AFR exome
AF:
0.124
Gnomad AMR exome
AF:
0.0978
Gnomad ASJ exome
AF:
0.104
Gnomad EAS exome
AF:
0.0865
Gnomad SAS exome
AF:
0.116
Gnomad FIN exome
AF:
0.182
Gnomad NFE exome
AF:
0.143
Gnomad OTH exome
AF:
0.122
GnomAD4 exome
AF:
0.141
AC:
205242
AN:
1456110
Hom.:
14723
AF XY:
0.141
AC XY:
101870
AN XY:
724748
show subpopulations
Gnomad4 AFR exome
AF:
0.124
Gnomad4 AMR exome
AF:
0.0984
Gnomad4 ASJ exome
AF:
0.111
Gnomad4 EAS exome
AF:
0.129
Gnomad4 SAS exome
AF:
0.118
Gnomad4 FIN exome
AF:
0.175
Gnomad4 NFE exome
AF:
0.146
Gnomad4 OTH exome
AF:
0.125
Alfa
AF:
0.129
Hom.:
3069
Bravo
AF:
0.124
Asia WGS
AF:
0.172
AC:
598
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
2.0
Dann
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs2075650; hg19: chr19-45395619; COSMIC: COSV52977687; COSMIC: COSV52977687; API