rs10124033

Variant names:

• chr9-96851822-G-A
• rs10124033
• NM_001001662.3:c.15+125C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-96851822-G-A
• chr9-96851822-G-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.15+125C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 1,003,056 control chromosomes in the GnomAD database, including 10,953 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 0.17 (5064 hom., cov: 32)
  • Exomes 𝑓: 0.057 (5889 hom.)
• Consequence: ZNF782 NM_001001662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001662.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF782	NM_001001662.3	MANE Select	c.15+125C>T		intron	N/A	NP_001001662.1
	ZNF782	NM_001346991.2		c.15+125C>T		intron	N/A	NP_001333920.1
	ZNF782	NM_001346993.2		c.-58+2266C>T		intron	N/A	NP_001333922.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF782	ENST00000481138.6	TSL:1 MANE Select	c.15+125C>T		intron	N/A	ENSP00000419397.1
	ZNF782	ENST00000535338.5	TSL:3	c.15+125C>T		intron	N/A	ENSP00000440624.2
	ZNF782	ENST00000478850.5	TSL:5	c.15+125C>T		intron	N/A	ENSP00000417577.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25207 AN: 152000 Hom.: 5027 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.114

GnomAD4 exome AF: 0.0569 AC: 48421 AN: 850938 Hom.: 5889 AF XY: 0.0569 AC XY: 25075 AN XY: 441026

African (AFR) AF: 0.476 AC: 9816 AN: 20626

American (AMR) AF: 0.0543 AC: 1848 AN: 34050

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 501 AN: 19294

East Asian (EAS) AF: 0.374 AC: 13144 AN: 35138

South Asian (SAS) AF: 0.110 AC: 6867 AN: 62294

European-Finnish (FIN) AF: 0.0834 AC: 3723 AN: 44650

Middle Eastern (MID) AF: 0.0687 AC: 299 AN: 4354

European-Non Finnish (NFE) AF: 0.0154 AC: 9113 AN: 590814

Other (OTH) AF: 0.0783 AC: 3110 AN: 39718

GnomAD4 genome AF: 0.166 AC: 25284 AN: 152118 Hom.: 5064 Cov.: 32 AF XY: 0.169 AC XY: 12573 AN XY: 74392

African (AFR) AF: 0.466 AC: 19325 AN: 41460

American (AMR) AF: 0.0768 AC: 1173 AN: 15278

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

East Asian (EAS) AF: 0.341 AC: 1766 AN: 5174

South Asian (SAS) AF: 0.115 AC: 555 AN: 4812

European-Finnish (FIN) AF: 0.0923 AC: 977 AN: 10590

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1128 AN: 68014

Other (OTH) AF: 0.113 AC: 239 AN: 2116

Alfa AF: 0.122 Hom.: 649

Bravo AF: 0.179

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.54
PhyloP100		-0.39
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: rs10124033; hg19: chr9-99614104;