Variant 5-43609170-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_182977.3(NNT):c.-26T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 1,583,958 control chromosomes in the GnomAD database, including 79,343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 5432 hom., cov: 32)

Exomes 𝑓: 0.31 ( 73911 hom. )

Consequence

NNT
NM_182977.3 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.312

Variant links:

Genes affected

NNT (HGNC:7863): (nicotinamide nucleotide transhydrogenase) This gene encodes an integral protein of the inner mitochondrial membrane. The enzyme couples hydride transfer between NAD(H) and NADP(+) to proton translocation across the inner mitochondrial membrane. Under most physiological conditions, the enzyme uses energy from the mitochondrial proton gradient to produce high concentrations of NADPH. The resulting NADPH is used for biosynthesis and in free radical detoxification. [provided by RefSeq, Sep 2016]

NNT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 5-43609170-T-C is Benign according to our data. Variant chr5-43609170-T-C is described in ClinVar as [Benign]. Clinvar id is 1325907.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NNT	NM_182977.3 linkuse as main transcript	c.-26T>C		5_prime_UTR_variant	2/22	ENST00000344920.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NNT	ENST00000344920.9 linkuse as main transcript	c.-26T>C		5_prime_UTR_variant	2/22	1	NM_182977.3	P1

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36113

AN:

151920

Hom.:

5434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0632

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.0665

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.276

GnomAD3 exomes

AF:

0.263

AC:

63154

AN:

240306

Hom.:

9702

AF XY:

0.273

AC XY:

35337

AN XY:

129600

show subpopulations

Gnomad AFR exome

AF:

0.0558

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.366

Gnomad EAS exome

AF:

0.0641

Gnomad SAS exome

AF:

0.243

Gnomad FIN exome

AF:

0.344

Gnomad NFE exome

AF:

0.329

Gnomad OTH exome

AF:

0.304

GnomAD4 exome

AF:

0.313

AC:

447802

AN:

1431920

Hom.:

73911

Cov.:

AF XY:

0.312

AC XY:

221368

AN XY:

709486

show subpopulations

Gnomad4 AFR exome

AF:

0.0545

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.372

Gnomad4 EAS exome

AF:

0.0956

Gnomad4 SAS exome

AF:

0.245

Gnomad4 FIN exome

AF:

0.343

Gnomad4 NFE exome

AF:

0.336

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.237

AC:

36103

AN:

152038

Hom.:

5432

Cov.:

AF XY:

0.236

AC XY:

17517

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.0631

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.355

Gnomad4 EAS

AF:

0.0667

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.332

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.301

Hom.:

6228

Bravo

AF:

0.224

Asia WGS

AF:

0.152

AC:

529

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Glucocorticoid deficiency 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.8

DANN

Benign

0.64

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over