Variant 16-30985474-C-T 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_025193.4(HSD3B7):c.-7+177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 1,486,078 control chromosomes in the GnomAD database, including 7,667 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 479 hom., cov: 33)

Exomes 𝑓: 0.099 ( 7188 hom. )

Consequence

HSD3B7
NM_025193.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.15

Variant links:

Genes affected

HSD3B7 (HGNC:18324): (hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7) This gene encodes an enzyme which is involved in the initial stages of the synthesis of bile acids from cholesterol and a member of the short-chain dehydrogenase/reductase superfamily. The encoded protein is a membrane-associated endoplasmic reticulum protein which is active against 7-alpha hydrosylated sterol substrates. Mutations in this gene are associated with a congenital bile acid synthesis defect which leads to neonatal cholestasis, a form of progressive liver disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

HSD3B7 links:

(HGNC:):

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=-0.91).

BP6

Variant 16-30985474-C-T is Benign according to our data. Variant chr16-30985474-C-T is described in ClinVar as [Benign]. Clinvar id is 1281644.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD3B7	NM_025193.4 linkuse as main transcript	c.-7+177C>T		intron_variant		ENST00000297679.10	NP_079469.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD3B7	ENST00000297679.10 linkuse as main transcript	c.-7+177C>T		intron_variant		1	NM_025193.4	ENSP00000297679	P1	Q9H2F3-1
	ENST00000624286.1 linkuse as main transcript	n.2797G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0684

AC:

10417

AN:

152184

Hom.:

479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0193

Gnomad AMI

AF:

0.0253

Gnomad AMR

AF:

0.0519

Gnomad ASJ

AF:

0.0677

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0362

Gnomad FIN

AF:

0.0689

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.0636

GnomAD3 exomes

AF:

0.0636

AC:

6559

AN:

103194

Hom.:

290

AF XY:

0.0651

AC XY:

3502

AN XY:

53824

show subpopulations

Gnomad AFR exome

AF:

0.0168

Gnomad AMR exome

AF:

0.0374

Gnomad ASJ exome

AF:

0.0768

Gnomad EAS exome

AF:

0.000391

Gnomad SAS exome

AF:

0.0346

Gnomad FIN exome

AF:

0.0638

Gnomad NFE exome

AF:

0.110

Gnomad OTH exome

AF:

0.0731

GnomAD4 exome

AF:

0.0986

AC:

131478

AN:

1333776

Hom.:

7188

Cov.:

AF XY:

0.0964

AC XY:

62865

AN XY:

652024

show subpopulations

Gnomad4 AFR exome

AF:

0.0164

Gnomad4 AMR exome

AF:

0.0401

Gnomad4 ASJ exome

AF:

0.0719

Gnomad4 EAS exome

AF:

0.000313

Gnomad4 SAS exome

AF:

0.0371

Gnomad4 FIN exome

AF:

0.0688

Gnomad4 NFE exome

AF:

0.112

Gnomad4 OTH exome

AF:

0.0851

GnomAD4 genome

AF:

0.0684

AC:

10412

AN:

152302

Hom.:

479

Cov.:

AF XY:

0.0655

AC XY:

4879

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0192

Gnomad4 AMR

AF:

0.0518

Gnomad4 ASJ

AF:

0.0677

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0361

Gnomad4 FIN

AF:

0.0689

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.0630

Alfa

AF:

0.0819

Hom.:

157

Bravo

AF:

0.0654

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.68

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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