chr17-49312652-G-C

Variant names:

• chr17-49312652-G-C
• rs2072153
• NM_001145365.3:c.1048+46C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 44 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]

FLJ40194 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF652	NM_001145365.3	c.1048+46C>G		intron_variant	Intron 3 of 5	ENST00000430262.3	NP_001138837.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF652	ENST00000430262.3	c.1048+46C>G		intron_variant	Intron 3 of 5	1	NM_001145365.3	ENSP00000416305.2
ZNF652	ENST00000362063.6	c.1048+46C>G		intron_variant	Intron 3 of 5	1		ENSP00000354686.2
ZNF652	ENST00000508237.5	n.508+46C>G		intron_variant	Intron 4 of 7	2		ENSP00000424848.1
FLJ40194	ENST00000655089.1	n.864-4939G>C		intron_variant	Intron 4 of 5

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

GnomAD2 exomes AF: 0.329 AC: 77131 AN: 234156 AF XY: 0.332

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 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

African (AFR) AF: 0.278 AC: 9074 AN: 32668

American (AMR) AF: 0.385 AC: 16378 AN: 42522

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 10191 AN: 24682

East Asian (EAS) AF: 0.366 AC: 14489 AN: 39536

South Asian (SAS) AF: 0.437 AC: 35869 AN: 82078

European-Finnish (FIN) AF: 0.272 AC: 14019 AN: 51486

Middle Eastern (MID) AF: 0.373 AC: 1668 AN: 4474

European-Non Finnish (NFE) AF: 0.309 AC: 340381 AN: 1101068

Other (OTH) AF: 0.326 AC: 19349 AN: 59270

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

African (AFR) AF: 0.274 AC: 11346 AN: 41462

American (AMR) AF: 0.348 AC: 5304 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1431 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1576 AN: 5184

South Asian (SAS) AF: 0.423 AC: 2040 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2852 AN: 10544

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.300 AC: 20407 AN: 67970

Other (OTH) AF: 0.300 AC: 635 AN: 2114

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
PhyloP100		-0.011
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2072153; hg19: chr17-47390014; COSMIC: COSV62947166;