dbSNP rs1050301: IMMT:p.Pro124Ser (chr2-86173701-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006839.3(IMMT):c.370C>T(p.Pro124Ser) variant causes a missense change. The variant allele was found at a frequency of 0.337 in 1,598,506 control chromosomes in the GnomAD database, including 96,177 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.28 ( 7133 hom., cov: 32)

Exomes 𝑓: 0.34 ( 89044 hom. )

Consequence

IMMT
NM_006839.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.14

Variant links:

Genes affected

IMMT (HGNC:6047): (inner membrane mitochondrial protein) Enables RNA binding activity. Involved in cristae formation. Located in mitochondrial inner membrane. Part of MICOS complex. [provided by Alliance of Genome Resources, Apr 2022]

IMMT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.4006786E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMMT	NM_006839.3 link	c.370C>T	p.Pro124Ser	missense_variant	Exon 4 of 15	ENST00000410111.8	NP_006830.2	Q16891-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMMT	ENST00000410111.8 link	c.370C>T	p.Pro124Ser	missense_variant	Exon 4 of 15	1	NM_006839.3	ENSP00000387262.3		Q16891-1

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42308

AN:

151994

Hom.:

7129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0792

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.319

GnomAD3 exomes

AF:

0.364

AC:

89785

AN:

246872

Hom.:

17591

AF XY:

0.368

AC XY:

49266

AN XY:

133952

show subpopulations

Gnomad AFR exome

AF:

0.0698

Gnomad AMR exome

AF:

0.443

Gnomad ASJ exome

AF:

0.395

Gnomad EAS exome

AF:

0.513

Gnomad SAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.337

Gnomad OTH exome

AF:

0.378

GnomAD4 exome

AF:

0.343

AC:

496621

AN:

1446394

Hom.:

89044

Cov.:

AF XY:

0.347

AC XY:

249730

AN XY:

720206

show subpopulations

Gnomad4 AFR exome

AF:

0.0650

Gnomad4 AMR exome

AF:

0.436

Gnomad4 ASJ exome

AF:

0.397

Gnomad4 EAS exome

AF:

0.491

Gnomad4 SAS exome

AF:

0.433

Gnomad4 FIN exome

AF:

0.339

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.345

GnomAD4 genome

AF:

0.278

AC:

42319

AN:

152112

Hom.:

7133

Cov.:

AF XY:

0.285

AC XY:

21158

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0790

Gnomad4 AMR

AF:

0.363

Gnomad4 ASJ

AF:

0.394

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.442

Gnomad4 FIN

AF:

0.353

Gnomad4 NFE

AF:

0.334

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.312

Hom.:

4661

Bravo

AF:

0.275

TwinsUK

AF:

0.333

AC:

1235

ALSPAC

AF:

0.330

AC:

1271

ESP6500AA

AF:

0.0905

AC:

331

ESP6500EA

AF:

0.337

AC:

2750

ExAC

AF:

0.358

AC:

43296

Asia WGS

AF:

0.431

AC:

1497

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.44

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.027

T;.;T;.;T;.

Eigen

Uncertain

0.24

Eigen_PC

Uncertain

0.25

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.73

T;T;T;T;T;T

MetaRNN

Benign

0.00084

T;T;T;T;T;T

MetaSVM

Benign

-0.90

PrimateAI

Benign

0.38

PROVEAN

Uncertain

-3.2

D;D;D;D;D;.

REVEL

Benign

0.12

Sift

Uncertain

0.014

D;D;T;T;T;.

Sift4G

Benign

0.15

T;T;T;T;T;D

Polyphen

0.94, 0.95, 0.75

.;P;P;.;P;.

Vest4

0.39

MPC

0.45

ClinPred

0.025

GERP RS

3.4

Varity_R

0.086

gMVP

0.48

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over