rs7760

Positions:

• chr8-94926194-C-A
• chr8-94926194-C-G
• chr8-94926194-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_033285.4(TP53INP1):​c.*4285G>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.817 in 152,494 control chromosomes in the GnomAD database, including 51,928 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 0.82 (51749 hom., cov: 31)
  • Exomes 𝑓: 0.91 (179 hom.)
• Consequence: TP53INP1 NM_033285.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.64

Genes affected

TP53INP1 (HGNC:18022): (tumor protein p53 inducible nuclear protein 1) Predicted to enable antioxidant activity. Involved in autophagic cell death; positive regulation of autophagy; and positive regulation of transcription, DNA-templated. Located in autophagosome; cytosol; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

NDUFAF6 (HGNC:28625): (NADH:ubiquinone oxidoreductase complex assembly factor 6) This gene encodes a protein that localizes to mitochondria and contains a predicted phytoene synthase domain. The encoded protein plays an important role in the assembly of complex I (NADH-ubiquinone oxidoreductase) of the mitochondrial respiratory chain through regulation of subunit ND1 biogenesis. Mutations in this gene are associated with complex I enzymatic deficiency. [provided by RefSeq, Nov 2011]

NDUFAF6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TP53INP1	NM_033285.4	c.*4285G>T		3_prime_UTR_variant	4/4	ENST00000342697.5	NP_150601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TP53INP1	ENST00000342697.5	c.*4285G>T		3_prime_UTR_variant	4/4	1	NM_033285.4	ENSP00000344215.4

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124175 AN: 151946 Hom.: 51717 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.822

GnomAD4 exome AF: 0.909 AC: 391 AN: 430 Hom.: 179 Cov.: 0 AF XY: 0.915 AC XY: 236 AN XY: 258

Gnomad4 FIN exome AF: 0.910

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.817 AC: 124257 AN: 152064 Hom.: 51749 Cov.: 31 AF XY: 0.821 AC XY: 61050 AN XY: 74334

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.819

Alfa AF: 0.873 Hom.: 65580

Bravo AF: 0.805

Asia WGS AF: 0.861 AC: 2993 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
DANN	Benign	0.87

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

Other links and lift over

dbSNP: rs7760; hg19: chr8-95938422;