Variant chr7-149847808-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001099220.3(ZNF862):c.315G>A(p.Pro105=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00803 in 1,613,788 control chromosomes in the GnomAD database, including 165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0058 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0083 ( 157 hom. )

Consequence

ZNF862
NM_001099220.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.48

Variant links:

Genes affected

ZNF862 (HGNC:34519): (zinc finger protein 862) Predicted to enable metal ion binding activity and protein dimerization activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF862 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 7-149847808-G-A is Benign according to our data. Variant chr7-149847808-G-A is described in ClinVar as [Benign]. Clinvar id is 781916.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.48 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00577 (878/152234) while in subpopulation SAS AF= 0.0382 (184/4818). AF 95% confidence interval is 0.0337. There are 8 homozygotes in gnomad4. There are 460 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF862	NM_001099220.3 linkuse as main transcript	c.315G>A	p.Pro105=	synonymous_variant	4/8	ENST00000223210.5	NP_001092690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF862	ENST00000223210.5 linkuse as main transcript	c.315G>A	p.Pro105=	synonymous_variant	4/8	5	NM_001099220.3	ENSP00000223210	P1	O60290-1
ZNF862	ENST00000460379.1 linkuse as main transcript	c.63G>A	p.Pro21=	synonymous_variant	4/4	4		ENSP00000417450

Frequencies

GnomAD3 genomes

AF:

0.00579

AC:

880

AN:

152116

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00334

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0386

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00734

Gnomad OTH

AF:

0.00716

GnomAD3 exomes

AF:

0.00912

AC:

2269

AN:

248784

Hom.:

AF XY:

0.0110

AC XY:

1482

AN XY:

134994

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00255

Gnomad ASJ exome

AF:

0.0108

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0419

Gnomad FIN exome

AF:

0.00200

Gnomad NFE exome

AF:

0.00602

Gnomad OTH exome

AF:

0.00845

GnomAD4 exome

AF:

0.00827

AC:

12085

AN:

1461554

Hom.:

157

Cov.:

AF XY:

0.00926

AC XY:

6733

AN XY:

727040

show subpopulations

Gnomad4 AFR exome

AF:

0.000777

Gnomad4 AMR exome

AF:

0.00300

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0413

Gnomad4 FIN exome

AF:

0.00249

Gnomad4 NFE exome

AF:

0.00660

Gnomad4 OTH exome

AF:

0.00878

GnomAD4 genome

AF:

0.00577

AC:

878

AN:

152234

Hom.:

Cov.:

AF XY:

0.00618

AC XY:

460

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.00144

Gnomad4 AMR

AF:

0.00334

Gnomad4 ASJ

AF:

0.0101

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0382

Gnomad4 FIN

AF:

0.00292

Gnomad4 NFE

AF:

0.00734

Gnomad4 OTH

AF:

0.00709

Alfa

AF:

0.00617

Hom.:

Bravo

AF:

0.00446

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.00840

EpiControl

AF:

0.00652

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	Labcorp Genetics (formerly Invitae), Labcorp	May 16, 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

-0.86

CADD

Benign

1.2

DANN

Benign

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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