rs3989699

chr8-7361099-C-Gchr8-7361099-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0490

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 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_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF705G	NM_001164457.3	c.139+11G>C		intron_variant		ENST00000400156.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF705G	ENST00000400156.4	c.139+11G>C		intron_variant		2	NM_001164457.3	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 58653 AN: 146736 Hom.: 5372 Cov.: 38 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.: 98 AF XY: 0.350 AC XY: 229419 AN XY: 655796

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.: 38 AF XY: 0.399 AC XY: 28667 AN XY: 71818

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

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 -

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

Other links and lift over

dbSNP: rs3989699; hg19: chr8-7218621; COSMIC: COSV67950347;