NM_001001662.3:c.245-1408G>C

Variant names:

• chr9-96821186-C-G
• rs12236125
• NM_001001662.3:c.245-1408G>C

Variant summary

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

The NM_001001662.3(ZNF782):​c.245-1408G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,126 control chromosomes in the GnomAD database, including 3,238 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 0.13 (3238 hom., cov: 32)
• Consequence: ZNF782 NM_001001662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF782	NM_001001662.3	c.245-1408G>C		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.245-1408G>C		intron_variant	Intron 5 of 5	1	NM_001001662.3	ENSP00000419397.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20066 AN: 152008 Hom.: 3207 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.0706

Gnomad FIN AF: 0.0455

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.132 AC: 20137 AN: 152126 Hom.: 3238 Cov.: 32 AF XY: 0.133 AC XY: 9888 AN XY: 74376

African (AFR) AF: 0.380 AC: 15745 AN: 41434

American (AMR) AF: 0.0672 AC: 1027 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1220 AN: 5164

South Asian (SAS) AF: 0.0700 AC: 338 AN: 4828

European-Finnish (FIN) AF: 0.0455 AC: 482 AN: 10596

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1030 AN: 68020

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0103 Hom.: 8

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.39
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: rs12236125; hg19: chr9-99583468;