rs79670217

Variant names:

• chr17-49337732-T-G
• rs79670217
• NM_001145365.3:c.-258-19749A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145365.3(ZNF652):​c.-258-19749A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.036 in 152,304 control chromosomes in the GnomAD database, including 139 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 0.036 (139 hom., cov: 31)
• Consequence: ZNF652 NM_001145365.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 1 publications found

Genes affected

ZNF652 (HGNC:29147): (zinc finger protein 652) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145365.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF652	NM_001145365.3	MANE Select	c.-258-19749A>C		intron	N/A	NP_001138837.1	Q9Y2D9
	ZNF652	NM_014897.2		c.-258-19749A>C		intron	N/A	NP_055712.1	Q9Y2D9
	ZNF652	NR_135579.2		n.343-15224A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF652	ENST00000430262.3	TSL:1 MANE Select	c.-258-19749A>C		intron	N/A	ENSP00000416305.2	Q9Y2D9
	ZNF652	ENST00000362063.6	TSL:1	c.-258-19749A>C		intron	N/A	ENSP00000354686.2	Q9Y2D9
	ZNF652	ENST00000949719.1		c.-258-19749A>C		intron	N/A	ENSP00000619778.1

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5484 AN: 152186 Hom.: 138 Cov.: 31

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0453

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0360 AC: 5485 AN: 152304 Hom.: 139 Cov.: 31 AF XY: 0.0352 AC XY: 2623 AN XY: 74466

African (AFR) AF: 0.0106 AC: 442 AN: 41574

American (AMR) AF: 0.0450 AC: 688 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4822

European-Finnish (FIN) AF: 0.0453 AC: 481 AN: 10622

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0530 AC: 3604 AN: 68018

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0473 Hom.: 331

Bravo AF: 0.0357

Asia WGS AF: 0.00897 AC: 31 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs79670217; hg19: chr17-47415094;