19-30490160-CTT-CT

Variant names:

• chr19-30490160-CT-C
• rs3837960
• NM_014717.3:c.2170+44438delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_014717.3(ZNF536):​c.2170+44438delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.024 in 150,010 control chromosomes in the GnomAD database, including 97 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.024 (97 hom., cov: 32)
• Consequence: ZNF536 NM_014717.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0749 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014717.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF536	NM_014717.3	MANE Select	c.2170+44438delT		intron	N/A	NP_055532.1	O15090
	ZNF536	NM_001376110.1		c.2170+44438delT		intron	N/A	NP_001363039.1	K7EQN6
	ZNF536	NM_001376111.1		c.2170+44438delT		intron	N/A	NP_001363040.1	K7EQN6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF536	ENST00000355537.4	TSL:1 MANE Select	c.2170+44429delT		intron	N/A	ENSP00000347730.1	O15090
	ZNF536	ENST00000592773.3	TSL:5	c.2170+44429delT		intron	N/A	ENSP00000467909.3	K7EQN6
	ZNF536	ENST00000706148.1		c.2170+44429delT		intron	N/A	ENSP00000516231.1	A0A994J7Z0

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3573 AN: 149904 Hom.: 94 Cov.: 32

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00766

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.00251

Gnomad OTH AF: 0.0161

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

GnomAD4 genome AF: 0.0240 AC: 3594 AN: 150010 Hom.: 97 Cov.: 32 AF XY: 0.0250 AC XY: 1831 AN XY: 73148

African (AFR) AF: 0.0598 AC: 2452 AN: 41014

American (AMR) AF: 0.00765 AC: 115 AN: 15034

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 76 AN: 3424

East Asian (EAS) AF: 0.0813 AC: 416 AN: 5116

South Asian (SAS) AF: 0.0207 AC: 98 AN: 4734

European-Finnish (FIN) AF: 0.0226 AC: 228 AN: 10110

Middle Eastern (MID) AF: 0.0139 AC: 4 AN: 288

European-Non Finnish (NFE) AF: 0.00251 AC: 169 AN: 67306

Other (OTH) AF: 0.0174 AC: 36 AN: 2074

Alfa AF: 0.000499 Hom.: 0

Bravo AF: 0.0247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.63
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: rs3837960; hg19: chr19-30981067;