dbSNP rs3989699: ZNF705G:c.139+11G>C (chr8-7361099-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_001164457.3(ZNF705G):c.139+11G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 5395 hom., cov: 38)

Exomes 𝑓: 0.35 ( 8899 hom. )

Failed GnomAD Quality Control

Consequence

ZNF705G
NM_001164457.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0490

Variant links:

Genes affected

ZNF705G (HGNC:37134): (zinc finger protein 705G) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF705G links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BP6

Variant 8-7361099-C-G is Benign according to our data. Variant chr8-7361099-C-G is described in ClinVar as [Benign]. Clinvar id is 403627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF705G	NM_001164457.3 link	c.139+11G>C		intron_variant	Intron 4 of 6	ENST00000400156.4	NP_001157929.1	A8MUZ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF705G	ENST00000400156.4 link	c.139+11G>C		intron_variant	Intron 4 of 6	2	NM_001164457.3	ENSP00000383020.4		A8MUZ8

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

58653

AN:

146736

Hom.:

5372

Cov.:

FAILED QC

Gnomad AFR

AF:

0.503

Gnomad AMI

AF:

0.383

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.271

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.383

Gnomad MID

AF:

0.365

Gnomad NFE

AF:

0.364

Gnomad OTH

AF:

0.398

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.351

AC:

460821

AN:

1311408

Hom.:

8899

Cov.:

AF XY:

0.350

AC XY:

229419

AN XY:

655796

show subpopulations

Gnomad4 AFR exome

AF:

0.521

Gnomad4 AMR exome

AF:

0.383

Gnomad4 ASJ exome

AF:

0.398

Gnomad4 EAS exome

AF:

0.270

Gnomad4 SAS exome

AF:

0.306

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.349

Gnomad4 OTH exome

AF:

0.359

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.400

AC:

58726

AN:

146854

Hom.:

5395

Cov.:

AF XY:

0.399

AC XY:

28667

AN XY:

71818

show subpopulations

Gnomad4 AFR

AF:

0.503

Gnomad4 AMR

AF:

0.382

Gnomad4 ASJ

AF:

0.402

Gnomad4 EAS

AF:

0.270

Gnomad4 SAS

AF:

0.311

Gnomad4 FIN

AF:

0.383

Gnomad4 NFE

AF:

0.364

Gnomad4 OTH

AF:

0.398

Alfa

AF:

0.315

Hom.:

132

Asia WGS

AF:

0.325

AC:

1131

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.0

DANN

Benign

0.47

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