rs2638094

Positions:

• chr11-6960257-A-G

Variant summary

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

The NM_001354854.1(ZNF215):​c.805+4475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,154 control chromosomes in the GnomAD database, including 2,163 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 0.16 (2163 hom., cov: 32)
• Consequence: ZNF215 NM_001354854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

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]

ZNF215 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF215	NM_001354854.1	c.805+4475A>G		intron_variant			NP_001341783.1
ZNF215	XM_024448683.2	c.805+4475A>G		intron_variant			XP_024304451.1
ZNF215	XM_047427571.1	c.805+4475A>G		intron_variant			XP_047283527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF215	ENST00000529903.1	c.805+4475A>G		intron_variant		1		ENSP00000432306.1
ZNF215	ENST00000610573.4	c.805+4475A>G		intron_variant		5		ENSP00000484674.1
ZNF215	ENST00000636097.1	n.*126+4475A>G		intron_variant		5		ENSP00000490414.1
ZNF215	ENST00000636606.1	n.*87+4475A>G		intron_variant		5		ENSP00000490359.1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23820 AN: 152036 Hom.: 2164 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.157 AC: 23822 AN: 152154 Hom.: 2163 Cov.: 32 AF XY: 0.153 AC XY: 11368 AN XY: 74390

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0508

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.163

Alfa AF: 0.182 Hom.: 1246

Bravo AF: 0.154

Asia WGS AF: 0.0350 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2638094; hg19: chr11-6981488;