rs584630

Variant names:

• chr10-38049771-A-C
• rs584630
• NM_006954.2:c.251-4604A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-38049771-A-C
• chr10-38049771-A-G

Variant summary

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

The NM_006954.2(ZNF33A):​c.251-4604A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,100 control chromosomes in the GnomAD database, including 59,166 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 0.88 (59166 hom., cov: 31)
• Consequence: ZNF33A NM_006954.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 2 publications found

Genes affected

ZNF33A (HGNC:13096): (zinc finger protein 33A) 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006954.2. 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
	ZNF33A	NM_006954.2	MANE Select	c.251-4604A>C		intron	N/A	NP_008885.1	Q06730-2
	ZNF33A	NM_001278177.2		c.314-4604A>C		intron	N/A	NP_001265106.1
	ZNF33A	NM_001278173.1		c.305-4604A>C		intron	N/A	NP_001265102.1	A0A0A0MR11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF33A	ENST00000432900.7	TSL:1 MANE Select	c.251-4604A>C		intron	N/A	ENSP00000402467.3	Q06730-2
	ZNF33A	ENST00000458705.6	TSL:1	c.251-4607A>C		intron	N/A	ENSP00000387713.2	Q06730-1
	ZNF33A	ENST00000307441.13	TSL:4	c.305-4604A>C		intron	N/A	ENSP00000304268.10	A0A0A0MR11

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133937 AN: 151982 Hom.: 59105 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.881 AC: 134057 AN: 152100 Hom.: 59166 Cov.: 31 AF XY: 0.883 AC XY: 65607 AN XY: 74330

African (AFR) AF: 0.917 AC: 38040 AN: 41498

American (AMR) AF: 0.836 AC: 12765 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.924 AC: 4774 AN: 5168

South Asian (SAS) AF: 0.937 AC: 4528 AN: 4832

European-Finnish (FIN) AF: 0.906 AC: 9585 AN: 10580

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58501 AN: 67958

Other (OTH) AF: 0.863 AC: 1822 AN: 2112

Alfa AF: 0.873 Hom.: 8534

Bravo AF: 0.873

Asia WGS AF: 0.928 AC: 3222 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.34
PhyloP100		-1.1
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: rs584630; hg19: chr10-38338699;