Variant 7-149776495-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The XM_047419936.1(ZNF467):c.-302C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00894 in 1,318,964 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0077 ( 11 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 76 hom. )

Consequence

ZNF467
XM_047419936.1 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.206

Variant links:

Genes affected

ZNF467 (HGNC:23154): (zinc finger protein 467) The protein encoded by this gene is a zinc finger protein whose function has not yet been elucidated in humans. However, the mouse ortholog of this protein enhances adipocyte differentiation and suppresses osteoblast differentiation in bone marrow. The mouse protein also is a transcription factor for several genes and can help recruit histone deacetylase complexes. [provided by RefSeq, Aug 2016]

ZNF467 links:

SSPOP (HGNC:):

SSPOP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0026706755).

BP6

Variant 7-149776495-G-A is Benign according to our data. Variant chr7-149776495-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658148.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein
ZNF467	XM_047419936.1 linkuse as main transcript	c.-302C>T	5_prime_UTR_premature_start_codon_gain_variant	1/5	XP_047275892.1
ZNF467	XM_047419936.1 linkuse as main transcript	c.-302C>T	5_prime_UTR_variant	1/5	XP_047275892.1
SSPOP	NR_163594.1 linkuse as main transcript	n.200G>A	non_coding_transcript_exon_variant	2/103

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSPOP	ENST00000378016.5 linkuse as main transcript	n.200G>A		non_coding_transcript_exon_variant	2/103	5
SSPOP	ENST00000486824.3 linkuse as main transcript	n.61G>A		non_coding_transcript_exon_variant	1/4	4

Frequencies

GnomAD3 genomes

AF:

0.00771

AC:

1173

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00150

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00687

Gnomad ASJ

AF:

0.0467

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.0206

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00873

Gnomad OTH

AF:

0.00718

GnomAD3 exomes

AF:

0.00996

AC:

1696

AN:

170320

Hom.:

AF XY:

0.00973

AC XY:

893

AN XY:

91804

show subpopulations

Gnomad AFR exome

AF:

0.00167

Gnomad AMR exome

AF:

0.00457

Gnomad ASJ exome

AF:

0.0520

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00162

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.0105

Gnomad OTH exome

AF:

0.0110

GnomAD4 exome

AF:

0.00910

AC:

10622

AN:

1166650

Hom.:

Cov.:

AF XY:

0.00890

AC XY:

5110

AN XY:

573950

show subpopulations

Gnomad4 AFR exome

AF:

0.000999

Gnomad4 AMR exome

AF:

0.00446

Gnomad4 ASJ exome

AF:

0.0494

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00159

Gnomad4 FIN exome

AF:

0.0179

Gnomad4 NFE exome

AF:

0.00919

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.00768

AC:

1170

AN:

152314

Hom.:

Cov.:

AF XY:

0.00792

AC XY:

590

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00149

Gnomad4 AMR

AF:

0.00686

Gnomad4 ASJ

AF:

0.0467

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0206

Gnomad4 NFE

AF:

0.00872

Gnomad4 OTH

AF:

0.00711

Alfa

AF:

0.0109

Hom.:

Bravo

AF:

0.00725

TwinsUK

AF:

0.00701

AC:

ALSPAC

AF:

0.00727

AC:

ESP6500AA

AF:

0.00214

AC:

ESP6500EA

AF:

0.0102

AC:

ExAC

AF:

0.00605

AC:

704

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

SSPOP: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.43

CADD

Benign

6.9

DANN

Benign

0.68

DEOGEN2

Benign

0.012

FATHMM_MKL

Benign

0.038

LIST_S2

Benign

0.53

MetaRNN

Benign

0.0027

MutationAssessor

Benign

1.5

PrimateAI

Benign

0.38

Sift4G

Uncertain

0.023

Polyphen

0.14

Vest4

0.14

MVP

0.095

GERP RS

0.72

Varity_R

0.088

gMVP

0.30

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