NM_001376110.1:c.3896-32743T>C

Variant names:

• chr19-30678014-T-C
• rs7258628
• NM_001376110.1:c.3896-32743T>C

Variant summary

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

The NM_001376110.1(ZNF536):​c.3896-32743T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,188 control chromosomes in the GnomAD database, including 616 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 0.067 (616 hom., cov: 33)
• Consequence: ZNF536 NM_001376110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF536	NM_001376110.1	c.3896-32743T>C		intron_variant	Intron 5 of 5		NP_001363039.1
ZNF536	NM_001376111.1	c.3896-32743T>C		intron_variant	Intron 5 of 5		NP_001363040.1
ZNF536	NM_001438953.1	c.3896-32743T>C		intron_variant	Intron 5 of 5		NP_001425882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF536	ENST00000592773.3	c.3896-32743T>C		intron_variant	Intron 5 of 5	5		ENSP00000467909.3
ZNF536	ENST00000706148.1	c.*27-32743T>C		intron_variant	Intron 6 of 6			ENSP00000516231.1
ZNF536	ENST00000706150.1	c.*27-32743T>C		intron_variant	Intron 5 of 5			ENSP00000516233.1

Frequencies

GnomAD3 genomes AF: 0.0671 AC: 10210 AN: 152070 Hom.: 608 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0680

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

GnomAD4 genome AF: 0.0673 AC: 10246 AN: 152188 Hom.: 616 Cov.: 33 AF XY: 0.0647 AC XY: 4818 AN XY: 74424

African (AFR) AF: 0.154 AC: 6398 AN: 41484

American (AMR) AF: 0.0450 AC: 688 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4822

European-Finnish (FIN) AF: 0.0150 AC: 159 AN: 10620

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2471 AN: 68014

Other (OTH) AF: 0.0673 AC: 142 AN: 2110

Alfa AF: 0.0448 Hom.: 631

Bravo AF: 0.0746

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.37
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7258628; hg19: chr19-31168921;