rs10404811

Variant names:

• chr19-57643439-T-C
• rs10404811
• NM_006385.5:c.*1258T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006385.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF211	NM_006385.5	MANE Select	c.*1258T>C		3_prime_UTR	Exon 4 of 4	NP_006376.2
	ZNF211	NR_049752.3		n.3447T>C		non_coding_transcript_exon	Exon 6 of 6
	ZNF211	NR_049753.3		n.3364T>C		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF211	ENST00000240731.5	TSL:2 MANE Select	c.*1258T>C		3_prime_UTR	Exon 4 of 4	ENSP00000240731.4

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

African (AFR) AF: 0.223 AC: 9257 AN: 41464

American (AMR) AF: 0.168 AC: 2570 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 765 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1654 AN: 5180

South Asian (SAS) AF: 0.200 AC: 966 AN: 4832

European-Finnish (FIN) AF: 0.142 AC: 1507 AN: 10602

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

European-Non Finnish (NFE) AF: 0.151 AC: 10297 AN: 67990

Other (OTH) AF: 0.202 AC: 426 AN: 2112

Alfa AF: 0.168 Hom.: 278

Bravo AF: 0.187

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.85
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs10404811; hg19: chr19-58154807;