chr8-7927044-C-T

Position:

• chr8-7927044-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001193630.1(ZNF705B):​c.-222+647C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 116,708 control chromosomes in the GnomAD database, including 8,906 homozygotes. 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: 𝑓 0.36 (8906 hom., cov: 25)
• Consequence: ZNF705B NM_001193630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

ZNF705B (HGNC:32284): (zinc finger protein 705B) 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]

LOC124901865 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF705B	NM_001193630.1	c.-222+647C>T		intron_variant		ENST00000400120.3	NP_001180559.1
ZNF705B	XM_047421207.1	c.-252+647C>T		intron_variant			XP_047277163.1
LOC124901865		n.7927044C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF705B	ENST00000400120.3	c.-222+647C>T		intron_variant		2	NM_001193630.1	ENSP00000382987.3

Frequencies

GnomAD3 genomes AF: 0.356 AC: 41497 AN: 116592 Hom.: 8908 Cov.: 25

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.374

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.356 AC: 41506 AN: 116708 Hom.: 8906 Cov.: 25 AF XY: 0.359 AC XY: 20223 AN XY: 56404

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.39

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: rs2698877; hg19: chr8-7784566;