rs937538

Variant names:

• chr12-133033656-T-C
• rs937538
• ENST00000443154.4:n.536-352A>G

Variant summary

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

The ENST00000701176.1(ZNF84-DT):​n.902A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 203,140 control chromosomes in the GnomAD database, including 21,275 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 0.45 (16115 hom., cov: 32)
  • Exomes 𝑓: 0.45 (5160 hom.)
• Consequence: ZNF84-DT ENST00000701176.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 5 publications found

Genes affected

ZNF84-DT (HGNC:53355): (ZNF84 divergent transcript)

PTP4A1P2 (HGNC:41929): (PTP4A1 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701176.1. 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
	ZNF84-DT	NR_110091.1		n.506-352A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF84-DT	ENST00000443154.4	TSL:1	n.536-352A>G		intron	N/A
	PTP4A1P2	ENST00000546033.1	TSL:6	n.154T>C		non_coding_transcript_exon	Exon 1 of 1
	ZNF84-DT	ENST00000701176.1		n.902A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68615 AN: 151944 Hom.: 16106 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.445 AC: 22736 AN: 51078 Hom.: 5160 Cov.: 0 AF XY: 0.444 AC XY: 13731 AN XY: 30920

African (AFR) AF: 0.621 AC: 467 AN: 752

American (AMR) AF: 0.348 AC: 743 AN: 2132

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 251 AN: 704

East Asian (EAS) AF: 0.256 AC: 423 AN: 1652

South Asian (SAS) AF: 0.475 AC: 3053 AN: 6432

European-Finnish (FIN) AF: 0.448 AC: 3983 AN: 8888

Middle Eastern (MID) AF: 0.341 AC: 47 AN: 138

European-Non Finnish (NFE) AF: 0.454 AC: 12779 AN: 28164

Other (OTH) AF: 0.447 AC: 990 AN: 2216

GnomAD4 genome AF: 0.451 AC: 68652 AN: 152062 Hom.: 16115 Cov.: 32 AF XY: 0.447 AC XY: 33234 AN XY: 74312

African (AFR) AF: 0.569 AC: 23592 AN: 41476

American (AMR) AF: 0.349 AC: 5337 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5164

South Asian (SAS) AF: 0.451 AC: 2179 AN: 4828

European-Finnish (FIN) AF: 0.438 AC: 4623 AN: 10552

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29172 AN: 67974

Other (OTH) AF: 0.392 AC: 826 AN: 2108

Alfa AF: 0.447 Hom.: 1688

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.1
DANN	Benign	0.63
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs937538;

hg19: chr12-133610242;