Variant 17-2057833-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_006497.4(HIC1):c.1143C>T(p.Ser381=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00238 in 1,577,628 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 34)

Exomes 𝑓: 0.0025 ( 7 hom. )

Consequence

HIC1
NM_006497.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.133

Variant links:

Genes affected

HIC1 (HGNC:4909): (HIC ZBTB transcriptional repressor 1) This gene functions as a growth regulatory and tumor repressor gene. Hypermethylation or deletion of the region of this gene have been associated with tumors and the contiguous-gene syndrome, Miller-Dieker syndrome. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2010]

HIC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 17-2057833-C-T is Benign according to our data. Variant chr17-2057833-C-T is described in ClinVar as [Benign]. Clinvar id is 712292.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.133 with no splicing effect.

BS2

High AC in GnomAd at 258 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIC1	NM_006497.4 linkuse as main transcript	c.1143C>T	p.Ser381=	synonymous_variant	2/2	ENST00000619757.5
HIC1	NM_001098202.1 linkuse as main transcript	c.1200C>T	p.Ser400=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIC1	ENST00000619757.5 linkuse as main transcript	c.1143C>T	p.Ser381=	synonymous_variant	2/2	1	NM_006497.4	P4	Q14526-2
HIC1	ENST00000399849.4 linkuse as main transcript	c.1143C>T	p.Ser381=	synonymous_variant	2/2	1		P4	Q14526-2
HIC1	ENST00000322941.3 linkuse as main transcript	c.1200C>T	p.Ser400=	synonymous_variant	2/2	5		A1	Q14526-1

Frequencies

GnomAD3 genomes

AF:

0.00170

AC:

258

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000603

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00131

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00300

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00132

AC:

246

AN:

186152

Hom.:

AF XY:

0.00137

AC XY:

140

AN XY:

102320

show subpopulations

Gnomad AFR exome

AF:

0.000411

Gnomad AMR exome

AF:

0.000892

Gnomad ASJ exome

AF:

0.000342

Gnomad EAS exome

AF:

0.0000697

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00257

Gnomad OTH exome

AF:

0.00144

GnomAD4 exome

AF:

0.00245

AC:

3499

AN:

1425316

Hom.:

Cov.:

AF XY:

0.00243

AC XY:

1717

AN XY:

706370

show subpopulations

Gnomad4 AFR exome

AF:

0.000490

Gnomad4 AMR exome

AF:

0.000897

Gnomad4 ASJ exome

AF:

0.000236

Gnomad4 EAS exome

AF:

0.0000263

Gnomad4 SAS exome

AF:

0.0000485

Gnomad4 FIN exome

AF:

0.0000651

Gnomad4 NFE exome

AF:

0.00302

Gnomad4 OTH exome

AF:

0.00215

GnomAD4 genome

AF:

0.00169

AC:

258

AN:

152312

Hom.:

Cov.:

AF XY:

0.00144

AC XY:

107

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000601

Gnomad4 AMR

AF:

0.00131

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00300

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00145

Hom.:

Bravo

AF:

0.00176

Asia WGS

AF:

0.000289

AC:

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

Invitae

Jan 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

Cadd

Benign

9.7

Dann

Benign

0.97

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

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