Variant 14-94768772-C-A 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_173849.3(GSC):c.616-123G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0331 in 1,407,968 control chromosomes in the GnomAD database, including 1,206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.045 ( 234 hom., cov: 33)

Exomes 𝑓: 0.032 ( 972 hom. )

Consequence

GSC
NM_173849.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0980

Variant links:

Genes affected

GSC (HGNC:4612): (goosecoid homeobox) This gene encodes a member of the bicoid subfamily of the paired (PRD) homeobox family of proteins. The encoded protein acts as a transcription factor and may be autoregulatory. A similar protein in mice plays a role in craniofacial and rib cage development during embryogenesis. [provided by RefSeq, Jul 2008]

GSC 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=-0.48).

BP6

Variant 14-94768772-C-A is Benign according to our data. Variant chr14-94768772-C-A is described in ClinVar as [Benign]. Clinvar id is 1291258.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSC	NM_173849.3 linkuse as main transcript	c.616-123G>T		intron_variant		ENST00000238558.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSC	ENST00000238558.5 linkuse as main transcript	c.616-123G>T		intron_variant		1	NM_173849.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0446

AC:

6794

AN:

152184

Hom.:

230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0735

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0363

Gnomad ASJ

AF:

0.0790

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.0149

Gnomad FIN

AF:

0.0203

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0267

Gnomad OTH

AF:

0.0474

GnomAD4 exome

AF:

0.0317

AC:

39837

AN:

1255664

Hom.:

972

AF XY:

0.0314

AC XY:

19740

AN XY:

629564

show subpopulations

Gnomad4 AFR exome

AF:

0.0783

Gnomad4 AMR exome

AF:

0.0310

Gnomad4 ASJ exome

AF:

0.0781

Gnomad4 EAS exome

AF:

0.136

Gnomad4 SAS exome

AF:

0.0170

Gnomad4 FIN exome

AF:

0.0231

Gnomad4 NFE exome

AF:

0.0262

Gnomad4 OTH exome

AF:

0.0387

GnomAD4 genome

AF:

0.0447

AC:

6815

AN:

152304

Hom.:

234

Cov.:

AF XY:

0.0440

AC XY:

3278

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0737

Gnomad4 AMR

AF:

0.0362

Gnomad4 ASJ

AF:

0.0790

Gnomad4 EAS

AF:

0.134

Gnomad4 SAS

AF:

0.0151

Gnomad4 FIN

AF:

0.0203

Gnomad4 NFE

AF:

0.0267

Gnomad4 OTH

AF:

0.0483

Alfa

AF:

0.0335

Hom.:

Bravo

AF:

0.0501

Asia WGS

AF:

0.0550

AC:

190

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

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.95

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