Genetic Variant NM_001002836.4:c.1086G>A (chr19-56088086-C-T) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_001002836.4(ZNF787):c.1086G>A(p.Glu362Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNF787
NM_001002836.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.41

Publications

2 publications found

Variant links:

Genes affected

ZNF787 (HGNC:26998): (zinc finger protein 787) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF787 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=-3.41 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF787	NM_001002836.4 link	c.1086G>A	p.Glu362Glu	synonymous_variant	Exon 3 of 3	ENST00000610935.2	NP_001002836.2	Q6DD87
ZNF787	XM_047438164.1 link	c.1086G>A	p.Glu362Glu	synonymous_variant	Exon 3 of 3		XP_047294120.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF787	ENST00000610935.2 link	c.1086G>A	p.Glu362Glu	synonymous_variant	Exon 3 of 3	1	NM_001002836.4	ENSP00000478557.1		Q6DD87

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1337444

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

664818

African (AFR)

AF:

0.00

AC:

AN:

27318

American (AMR)

AF:

0.00

AC:

AN:

25290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22598

East Asian (EAS)

AF:

0.00

AC:

AN:

26748

South Asian (SAS)

AF:

0.00

AC:

AN:

76524

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38272

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3892

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1062446

Other (OTH)

AF:

0.00

AC:

AN:

54356

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.061

(source)

DANN

Benign

0.95

PhyloP100

-3.4

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over