rs10404811

chr19-57643439-T-C

Variant summary

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

The NM_006385.5(ZNF211):c.*1258T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,148 control chromosomes in the GnomAD database, including 2,671 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 0.18 (2671 hom., cov: 32)
• Consequence: ZNF211 NM_006385.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

ZNF211 (HGNC:13003): (zinc finger protein 211) This gene encodes a protein containing a Kruppel-associated box domain and multiple zinc finger domains. This protein may play a role in developmental processes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF211	NM_006385.5	c.*1258T>C		3_prime_UTR_variant	4/4	ENST00000240731.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF211	ENST00000240731.5	c.*1258T>C		3_prime_UTR_variant	4/4	2	NM_006385.5	A2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27589 AN: 152030 Hom.: 2664 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.182 AC: 27644 AN: 152148 Hom.: 2671 Cov.: 32 AF XY: 0.182 AC XY: 13513 AN XY: 74394

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.202

Alfa AF: 0.166 Hom.: 262

Bravo AF: 0.187

Asia WGS AF: 0.255 AC: 887 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	5.7
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10404811; hg19: chr19-58154807;