Variant 7-75982438-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001395413.1(POR):c.821+116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 847,838 control chromosomes in the GnomAD database, including 38,174 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6141 hom., cov: 32)

Exomes 𝑓: 0.29 ( 32033 hom. )

Consequence

POR
NM_001395413.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.880

Variant links:

Genes affected

POR (HGNC:9208): (cytochrome p450 oxidoreductase) This gene encodes an endoplasmic reticulum membrane oxidoreductase that is essential for multiple metabolic processes, including reactions catalyzed by cytochrome P450 proteins for metabolism of steroid hormones, drugs and xenobiotics. The encoded protein has a flavin adenine dinucleotide (FAD)-binding domain and a flavodoxin-like domain which bind two cofactors, FAD and FMN, that allow it to donate electrons directly from NADPH to all microsomal P450 enzymes. Mutations in this gene cause a complex set of disorders, including apparent combined P450C17 and P450C21 deficiency, amenorrhea and disordered steroidogenesis, congenital adrenal hyperplasia and Antley-Bixler syndrome, that resemble those caused by defects in steroid metabolizing enzymes such as aromatase, 21-hydroxylase, and 17 alpha-hydroxylase. [provided by RefSeq, Aug 2020]

POR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 7-75982438-C-T is Benign according to our data. Variant chr7-75982438-C-T is described in ClinVar as [Benign]. Clinvar id is 1252414.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POR	NM_001395413.1 linkuse as main transcript	c.821+116C>T		intron_variant		ENST00000461988.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POR	ENST00000461988.6 linkuse as main transcript	c.821+116C>T		intron_variant		1	NM_001395413.1	P4

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41770

AN:

151892

Hom.:

6131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.293

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.279

GnomAD4 exome

AF:

0.295

AC:

205219

AN:

695828

Hom.:

32033

AF XY:

0.299

AC XY:

106906

AN XY:

357838

show subpopulations

Gnomad4 AFR exome

AF:

0.176

Gnomad4 AMR exome

AF:

0.286

Gnomad4 ASJ exome

AF:

0.285

Gnomad4 EAS exome

AF:

0.401

Gnomad4 SAS exome

AF:

0.352

Gnomad4 FIN exome

AF:

0.406

Gnomad4 NFE exome

AF:

0.278

Gnomad4 OTH exome

AF:

0.286

GnomAD4 genome

AF:

0.275

AC:

41809

AN:

152010

Hom.:

6141

Cov.:

AF XY:

0.284

AC XY:

21120

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.293

Gnomad4 ASJ

AF:

0.285

Gnomad4 EAS

AF:

0.382

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.289

Gnomad4 OTH

AF:

0.280

Alfa

AF:

0.273

Hom.:

916

Bravo

AF:

0.259

Asia WGS

AF:

0.336

AC:

1169

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.8

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

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