5-43612882-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_182977.3(NNT):c.152-26_152-25insA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.50 (18505 hom., cov: 0)
  • Exomes 𝑓: 0.46 (131295 hom.)
• Consequence: NNT NM_182977.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.110

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-43612882-T-TA is Benign according to our data. Variant chr5-43612882-T-TA is described in ClinVar as [Benign]. Clinvar id is 1325908.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NNT	NM_182977.3	c.152-26_152-25insA		intron_variant		ENST00000344920.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NNT	ENST00000344920.9	c.152-26_152-25insA		intron_variant		1	NM_182977.3	P1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 73155 AN: 145674 Hom.: 18511 Cov.: 0

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.537

GnomAD3 exomes AF: 0.447 AC: 93016 AN: 208318 Hom.: 21198 AF XY: 0.452 AC XY: 51300 AN XY: 113616

Gnomad AFR exome AF: 0.587

Gnomad AMR exome AF: 0.299

Gnomad ASJ exome AF: 0.539

Gnomad EAS exome AF: 0.113

Gnomad SAS exome AF: 0.400

Gnomad FIN exome AF: 0.461

Gnomad NFE exome AF: 0.507

Gnomad OTH exome AF: 0.498

GnomAD4 exome AF: 0.463 AC: 560001 AN: 1208838 Hom.: 131295 Cov.: 19 AF XY: 0.462 AC XY: 280752 AN XY: 607484

Gnomad4 AFR exome AF: 0.591

Gnomad4 AMR exome AF: 0.310

Gnomad4 ASJ exome AF: 0.525

Gnomad4 EAS exome AF: 0.120

Gnomad4 SAS exome AF: 0.375

Gnomad4 FIN exome AF: 0.443

Gnomad4 NFE exome AF: 0.485

Gnomad4 OTH exome AF: 0.472

GnomAD4 genome AF: 0.502 AC: 73169 AN: 145780 Hom.: 18505 Cov.: 0 AF XY: 0.494 AC XY: 35092 AN XY: 71062

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.535

Alfa AF: 0.456 Hom.: 1592

Asia WGS AF: 0.262 AC: 864 AN: 3284

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Glucocorticoid deficiency 4 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs139409541; hg19: chr5-43612984;