Variant 16-30985550-C-G 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.-6-103C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 1,531,530 control chromosomes in the GnomAD database, including 287,390 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 23377 hom., cov: 33)

Exomes 𝑓: 0.61 ( 264013 hom. )

Consequence

HSD3B7
NM_025193.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.785

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=-0.8).

BP6

Variant 16-30985550-C-G is Benign according to our data. Variant chr16-30985550-C-G is described in ClinVar as [Benign]. Clinvar id is 1225980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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.-6-103C>G		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.-6-103C>G		intron_variant		1	NM_025193.4	ENSP00000297679	P1	Q9H2F3-1
	ENST00000624286.1 linkuse as main transcript	n.2721G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.527

AC:

79954

AN:

151678

Hom.:

23361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.570

Gnomad ASJ

AF:

0.690

Gnomad EAS

AF:

0.905

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.664

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.593

GnomAD3 exomes

AF:

0.576

AC:

80893

AN:

140418

Hom.:

25228

AF XY:

0.564

AC XY:

42516

AN XY:

75362

show subpopulations

Gnomad AFR exome

AF:

0.249

Gnomad AMR exome

AF:

0.564

Gnomad ASJ exome

AF:

0.677

Gnomad EAS exome

AF:

0.909

Gnomad SAS exome

AF:

0.331

Gnomad FIN exome

AF:

0.648

Gnomad NFE exome

AF:

0.634

Gnomad OTH exome

AF:

0.611

GnomAD4 exome

AF:

0.610

AC:

841277

AN:

1379734

Hom.:

264013

Cov.:

AF XY:

0.604

AC XY:

411104

AN XY:

680688

show subpopulations

Gnomad4 AFR exome

AF:

0.260

Gnomad4 AMR exome

AF:

0.567

Gnomad4 ASJ exome

AF:

0.674

Gnomad4 EAS exome

AF:

0.909

Gnomad4 SAS exome

AF:

0.334

Gnomad4 FIN exome

AF:

0.649

Gnomad4 NFE exome

AF:

0.628

Gnomad4 OTH exome

AF:

0.609

GnomAD4 genome

AF:

0.527

AC:

80015

AN:

151796

Hom.:

23377

Cov.:

AF XY:

0.528

AC XY:

39136

AN XY:

74158

show subpopulations

Gnomad4 AFR

AF:

0.275

Gnomad4 AMR

AF:

0.570

Gnomad4 ASJ

AF:

0.690

Gnomad4 EAS

AF:

0.905

Gnomad4 SAS

AF:

0.309

Gnomad4 FIN

AF:

0.664

Gnomad4 NFE

AF:

0.625

Gnomad4 OTH

AF:

0.590

Alfa

AF:

0.520

Hom.:

2758

Bravo

AF:

0.519

Asia WGS

AF:

0.546

AC:

1902

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	clinical testing	GeneDx	Jul 09, 2018	- -
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

-0.80

CADD

Benign

3.1

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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