rs732531

Variant names:

• chr5-178910214-C-A
• rs732531
• NM_030613.4:c.-449-2370C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-178910214-C-A
• chr5-178910214-C-G
• chr5-178910214-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_030613.4(ZFP2):​c.-449-2370C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,561,932 control chromosomes in the GnomAD database, including 44,098 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 0.22 (3948 hom., cov: 32)
  • Exomes 𝑓: 0.23 (40150 hom.)
• Consequence: ZFP2 NM_030613.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525
• Publications: 3 publications found

Genes affected

ZFP2 (HGNC:26138): (ZFP2 zinc finger protein) 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000213328 (HGNC:):

ZNF454-DT (HGNC:55213): (ZNF454 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030613.4. 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
	ZFP2	NM_030613.4	MANE Select	c.-449-2370C>A		intron	N/A	NP_085116.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP2	ENST00000361362.7	TSL:1 MANE Select	c.-449-2370C>A		intron	N/A	ENSP00000354453.2
	ZFP2	ENST00000896567.1		c.-449-2370C>A		intron	N/A	ENSP00000566626.1
	ZFP2	ENST00000896568.1		c.-449-2370C>A		intron	N/A	ENSP00000566627.1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32929 AN: 152068 Hom.: 3948 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.232 AC: 327654 AN: 1409746 Hom.: 40150 Cov.: 29 AF XY: 0.233 AC XY: 163899 AN XY: 703202

African (AFR) AF: 0.119 AC: 3891 AN: 32774

American (AMR) AF: 0.217 AC: 9669 AN: 44472

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 5524 AN: 25458

East Asian (EAS) AF: 0.171 AC: 6733 AN: 39486

South Asian (SAS) AF: 0.205 AC: 17421 AN: 84826

European-Finnish (FIN) AF: 0.313 AC: 16581 AN: 52976

Middle Eastern (MID) AF: 0.222 AC: 1258 AN: 5666

European-Non Finnish (NFE) AF: 0.238 AC: 253482 AN: 1065606

Other (OTH) AF: 0.224 AC: 13095 AN: 58482

GnomAD4 genome AF: 0.216 AC: 32935 AN: 152186 Hom.: 3948 Cov.: 32 AF XY: 0.220 AC XY: 16336 AN XY: 74396

African (AFR) AF: 0.129 AC: 5358 AN: 41542

American (AMR) AF: 0.232 AC: 3549 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3466

East Asian (EAS) AF: 0.165 AC: 853 AN: 5176

South Asian (SAS) AF: 0.196 AC: 948 AN: 4826

European-Finnish (FIN) AF: 0.321 AC: 3398 AN: 10588

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17186 AN: 67994

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.224 Hom.: 10674

Bravo AF: 0.203

Asia WGS AF: 0.147 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	17
DANN	Benign	0.91
PhyloP100		0.53
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: rs732531; hg19: chr5-178337215; COSMIC: COSV63725136; COSMIC: COSV63725136;