rs2239730

Positions:

• chr11-6955944-G-C

Variant summary

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

The NM_013250.4(ZNF215):​c.967G>C​(p.Val323Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,612,506 control chromosomes in the GnomAD database, including 37,006 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.24 (4715 hom., cov: 33)
  • Exomes 𝑓: 0.20 (32291 hom.)
• Consequence: ZNF215 NM_013250.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

ZNF215 (HGNC:13007): (zinc finger protein 215) This gene is imprinted in a tissue-specific manner with preferential expression in the testis, and encodes a zinc finger protein that belongs to a family of zinc finger transcription factors. The encoded protein contains an N-terminal SRE-ZBP, Ctfin51, AW-1, and Number 18 (SCAN) domain, a kruppel-associated box A (KRABA) domain, and four C-terminal zinc finger domains. This gene is located within one of three regions on chromosome 11p15 associated with Beckwith-Wiedemann syndrome, called Beckwith-Wiedemann syndrome chromosome region-2 (BWSCR2), and is thought to play a role in the etiology of this disease. [provided by RefSeq, Aug 2017]

LOC102724711 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0039271414).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF215	NM_013250.4	c.967G>C	p.Val323Leu	missense_variant	7/7	ENST00000278319.10
LOC102724711	XR_002957236.2	n.1980-170C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF215	ENST00000278319.10	c.967G>C	p.Val323Leu	missense_variant	7/7	1	NM_013250.4	P1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36271 AN: 152000 Hom.: 4709 Cov.: 33

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.228

GnomAD3 exomes AF: 0.189 AC: 47091 AN: 249142 Hom.: 5098 AF XY: 0.184 AC XY: 24781 AN XY: 134980

Gnomad AFR exome AF: 0.343

Gnomad AMR exome AF: 0.112

Gnomad ASJ exome AF: 0.248

Gnomad EAS exome AF: 0.139

Gnomad SAS exome AF: 0.0773

Gnomad FIN exome AF: 0.232

Gnomad NFE exome AF: 0.214

Gnomad OTH exome AF: 0.205

GnomAD4 exome AF: 0.205 AC: 299208 AN: 1460388 Hom.: 32291 Cov.: 37 AF XY: 0.201 AC XY: 145823 AN XY: 726446

Gnomad4 AFR exome AF: 0.338

Gnomad4 AMR exome AF: 0.121

Gnomad4 ASJ exome AF: 0.249

Gnomad4 EAS exome AF: 0.153

Gnomad4 SAS exome AF: 0.0821

Gnomad4 FIN exome AF: 0.230

Gnomad4 NFE exome AF: 0.213

Gnomad4 OTH exome AF: 0.210

GnomAD4 genome AF: 0.239 AC: 36303 AN: 152118 Hom.: 4715 Cov.: 33 AF XY: 0.237 AC XY: 17627 AN XY: 74362

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.0818

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.226

Alfa AF: 0.216 Hom.: 2823

Bravo AF: 0.243

TwinsUK AF: 0.222 AC: 823

ALSPAC AF: 0.209 AC: 807

ESP6500AA AF: 0.335 AC: 1472

ESP6500EA AF: 0.213 AC: 1831

ExAC AF: 0.193 AC: 23418

Asia WGS AF: 0.115 AC: 402 AN: 3478

EpiCase AF: 0.223

EpiControl AF: 0.221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	-0.83	T
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.81
DEOGEN2	Benign	0.0011	T;T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.0021	N
MetaRNN	Benign	0.0039	T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.0	N;N
MutationTaster	Benign	1.0	P;P;P
PrimateAI	Benign	0.25	T
PROVEAN	Benign	0.090	N;N
REVEL	Benign	0.041
Sift	Benign	0.25	T;T
Sift4G	Benign	0.55	T;T
Polyphen		0.0	B;B
Vest4		0.011
MutPred		0.35		Loss of loop (P = 0.1242);Loss of loop (P = 0.1242);
MPC		0.0059
ClinPred		0.0047	T
GERP RS		2.5
Varity_R		0.046
gMVP		0.042

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: rs2239730; hg19: chr11-6977175; COSMIC: COSV53491730;