NM_014717.3:c.2324-3164C>G

Variant names:

• chr19-30544779-C-G
• rs10418356
• NM_014717.3:c.2324-3164C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014717.3(ZNF536):​c.2324-3164C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0536 in 152,260 control chromosomes in the GnomAD database, including 357 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 0.054 (357 hom., cov: 32)
• Consequence: ZNF536 NM_014717.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 1 publications found

Genes affected

ZNF536 (HGNC:29025): (zinc finger protein 536) The protein encoded by this gene is a highly conserved zinc finger protein. The encoded protein is most abundant in brain, where it negatively regulates neuronal differentiation. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF536	NM_014717.3	c.2324-3164C>G		intron_variant	Intron 3 of 4	ENST00000355537.4	NP_055532.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF536	ENST00000355537.4	c.2324-3164C>G		intron_variant	Intron 3 of 4	1	NM_014717.3	ENSP00000347730.1

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8163 AN: 152142 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0536 AC: 8166 AN: 152260 Hom.: 357 Cov.: 32 AF XY: 0.0535 AC XY: 3983 AN XY: 74444

African (AFR) AF: 0.103 AC: 4288 AN: 41536

American (AMR) AF: 0.0298 AC: 456 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3468

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5178

South Asian (SAS) AF: 0.122 AC: 586 AN: 4820

European-Finnish (FIN) AF: 0.0201 AC: 213 AN: 10614

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0354 AC: 2409 AN: 68026

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0514 Hom.: 33

Bravo AF: 0.0529

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.44
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10418356; hg19: chr19-31035686;