chr7-149201983-A-T

Position:

• chr7-149201983-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003575.4(ZNF282):​c.585+3231A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 151,760 control chromosomes in the GnomAD database, including 54,022 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 0.84 (54022 hom., cov: 27)
• Consequence: ZNF282 NM_003575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ZNF282 (HGNC:13076): (zinc finger protein 282) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF282	NM_003575.4	c.585+3231A>T		intron_variant		ENST00000610704.5	NP_003566.1
ZNF282	NM_001303481.3	c.585+3231A>T		intron_variant			NP_001290410.1
ZNF282	XM_006716151.5	c.585+3231A>T		intron_variant			XP_006716214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF282	ENST00000610704.5	c.585+3231A>T		intron_variant		1	NM_003575.4	ENSP00000477841.1
ZNF282	ENST00000479907.1	c.585+3231A>T		intron_variant		2		ENSP00000418840.1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127375 AN: 151642 Hom.: 53997 Cov.: 27

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.840 AC: 127452 AN: 151760 Hom.: 54022 Cov.: 27 AF XY: 0.844 AC XY: 62569 AN XY: 74150

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.860

Alfa AF: 0.865 Hom.: 6716

Bravo AF: 0.833

Asia WGS AF: 0.887 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1211759; hg19: chr7-148899075;