NM_001001662.3:c.245-2820C>T

Variant names:

• chr9-96822598-G-A
• rs7859940
• NM_001001662.3:c.245-2820C>T

Variant summary

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

The NM_001001662.3(ZNF782):​c.245-2820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,018 control chromosomes in the GnomAD database, including 8,353 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 0.21 (8353 hom., cov: 32)
• Consequence: ZNF782 NM_001001662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 5 publications found

Genes affected

ZNF782 (HGNC:33110): (zinc finger protein 782) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF782	NM_001001662.3	c.245-2820C>T		intron_variant	Intron 5 of 5	ENST00000481138.6	NP_001001662.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF782	ENST00000481138.6	c.245-2820C>T		intron_variant	Intron 5 of 5	1	NM_001001662.3	ENSP00000419397.1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32152 AN: 151900 Hom.: 8311 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0211

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.212 AC: 32242 AN: 152018 Hom.: 8353 Cov.: 32 AF XY: 0.215 AC XY: 15962 AN XY: 74296

African (AFR) AF: 0.610 AC: 25295 AN: 41466

American (AMR) AF: 0.0974 AC: 1489 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1760 AN: 5170

South Asian (SAS) AF: 0.116 AC: 559 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1255 AN: 10544

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0211 AC: 1435 AN: 67952

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.0670 Hom.: 1985

Bravo AF: 0.229

Asia WGS AF: 0.205 AC: 710 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		0.20
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: rs7859940; hg19: chr9-99584880;