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GeneBe

7-149847808-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.48 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
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
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF862NM_001099220.3 linkuse as main transcriptc.315G>A p.Pro105= synonymous_variant 4/8 ENST00000223210.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF862ENST00000223210.5 linkuse as main transcriptc.315G>A p.Pro105= synonymous_variant 4/85 NM_001099220.3 P1O60290-1
ZNF862ENST00000460379.1 linkuse as main transcriptc.63G>A p.Pro21= synonymous_variant 4/44

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00579
AC:
880
AN:
152116
Hom.:
8
Cov.:
32
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.:
43
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.:
32
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00577
AC:
878
AN:
152234
Hom.:
8
Cov.:
32
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.:
1
Bravo
AF:
0.00446
Asia WGS
AF:
0.0140
AC:
50
AN:
3478
EpiCase
AF:
0.00840
EpiControl
AF:
0.00652

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 submitterclinical testingInvitaeMay 16, 2018- -

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.

Other links and lift over

dbSNP: rs149637534; hg19: chr7-149544897; COSMIC: COSV56224477; COSMIC: COSV56224477; API