NM_006973.3:c.-69-259A>G

Variant names:

• chr10-43646461-T-C
• rs3814561
• NM_006973.3:c.-69-259A>G

Variant summary

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

The NM_006973.3(ZNF32):​c.-69-259A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,036 control chromosomes in the GnomAD database, including 6,725 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 0.29 (6725 hom., cov: 32)
• Consequence: ZNF32 NM_006973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 0 publications found

Genes affected

ZNF32 (HGNC:13095): (zinc finger protein 32) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF32-AS2 (HGNC:23593): (ZNF32 antisense RNA 2)

ZNF32-AS3 (HGNC:23583): (ZNF32 antisense RNA 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006973.3. 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
	ZNF32	NM_006973.3	MANE Select	c.-69-259A>G		intron	N/A	NP_008904.1	P17041
	ZNF32	NM_001324164.2		c.-163-259A>G		intron	N/A	NP_001311093.1
	ZNF32	NM_001324165.2		c.-163-259A>G		intron	N/A	NP_001311094.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF32	ENST00000374433.7	TSL:1 MANE Select	c.-69-259A>G		intron	N/A	ENSP00000363556.2	P17041
	ZNF32-AS2	ENST00000458063.1	TSL:1	n.162+17483T>C		intron	N/A
	ZNF32	ENST00000858679.1		c.-328A>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 2	ENSP00000528738.1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44261 AN: 151918 Hom.: 6723 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.291 AC: 44281 AN: 152036 Hom.: 6725 Cov.: 32 AF XY: 0.293 AC XY: 21779 AN XY: 74278

African (AFR) AF: 0.263 AC: 10931 AN: 41488

American (AMR) AF: 0.331 AC: 5057 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3468

East Asian (EAS) AF: 0.529 AC: 2726 AN: 5152

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4820

European-Finnish (FIN) AF: 0.256 AC: 2701 AN: 10556

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19296 AN: 67970

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.288 Hom.: 1048

Bravo AF: 0.295

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		0.14
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: rs3814561; hg19: chr10-44141909;