chr11-6941726-C-T

Variant names:

• chr11-6941726-C-T
• rs2857891
• NM_013250.4:c.483+73C>T

Variant summary

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

The NM_013250.4(ZNF215):​c.483+73C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,508,188 control chromosomes in the GnomAD database, including 28,650 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 (2259 hom., cov: 33)
  • Exomes 𝑓: 0.19 (26391 hom.)
• Consequence: ZNF215 NM_013250.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

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]

LOC107984019 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF215	NM_013250.4	c.483+73C>T		intron_variant	Intron 4 of 6	ENST00000278319.10	NP_037382.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF215	ENST00000278319.10	c.483+73C>T		intron_variant	Intron 4 of 6	1	NM_013250.4	ENSP00000278319.5

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24433 AN: 152090 Hom.: 2261 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.189 AC: 256025 AN: 1355980 Hom.: 26391 AF XY: 0.185 AC XY: 125193 AN XY: 675992

Gnomad4 AFR exome AF: 0.104

Gnomad4 AMR exome AF: 0.116

Gnomad4 ASJ exome AF: 0.218

Gnomad4 EAS exome AF: 0.00220

Gnomad4 SAS exome AF: 0.0598

Gnomad4 FIN exome AF: 0.173

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.161 AC: 24436 AN: 152208 Hom.: 2259 Cov.: 33 AF XY: 0.156 AC XY: 11641 AN XY: 74426

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0524

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.166

Alfa AF: 0.196 Hom.: 5210

Bravo AF: 0.159

Asia WGS AF: 0.0430 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.70

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: rs2857891; hg19: chr11-6962957;