17-49312652-G-C

Position:

• chr17-49312652-G-C

Variant summary

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

The NM_001145365.3(ZNF652):​c.1048+46C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 1,589,804 control chromosomes in the GnomAD database, including 82,716 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 0.30 (7210 hom., cov: 31)
  • Exomes 𝑓: 0.32 (75506 hom.)
• Consequence: ZNF652 NM_001145365.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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]

FLJ40194 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF652	NM_001145365.3	c.1048+46C>G		intron_variant		ENST00000430262.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF652	ENST00000430262.3	c.1048+46C>G		intron_variant		1	NM_001145365.3	P1
ZNF652	ENST00000362063.6	c.1048+46C>G		intron_variant		1		P1
FLJ40194	ENST00000655089.1	n.864-4939G>C		intron_variant, non_coding_transcript_variant
ZNF652	ENST00000508237.5	c.508+46C>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45979 AN: 151902 Hom.: 7198 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.301

GnomAD3 exomes AF: 0.329 AC: 77131 AN: 234156 Hom.: 13074 AF XY: 0.332 AC XY: 41880 AN XY: 126236

Gnomad AFR exome AF: 0.275

Gnomad AMR exome AF: 0.393

Gnomad ASJ exome AF: 0.403

Gnomad EAS exome AF: 0.288

Gnomad SAS exome AF: 0.429

Gnomad FIN exome AF: 0.270

Gnomad NFE exome AF: 0.305

Gnomad OTH exome AF: 0.337

GnomAD4 exome AF: 0.321 AC: 461418 AN: 1437784 Hom.: 75506 Cov.: 29 AF XY: 0.324 AC XY: 231327 AN XY: 714022

Gnomad4 AFR exome AF: 0.278

Gnomad4 AMR exome AF: 0.385

Gnomad4 ASJ exome AF: 0.413

Gnomad4 EAS exome AF: 0.366

Gnomad4 SAS exome AF: 0.437

Gnomad4 FIN exome AF: 0.272

Gnomad4 NFE exome AF: 0.309

Gnomad4 OTH exome AF: 0.326

GnomAD4 genome AF: 0.303 AC: 46035 AN: 152020 Hom.: 7210 Cov.: 31 AF XY: 0.307 AC XY: 22774 AN XY: 74274

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.300

Alfa AF: 0.289 Hom.: 3997

Bravo AF: 0.307

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.88
DANN	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2072153; hg19: chr17-47390014; COSMIC: COSV62947166;