rs1130241

Variant names:

• chr10-38059858-T-C
• rs1130241
• NM_006954.2:c.*3298T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006954.2(ZNF33A):​c.*3298T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ZNF33A NM_006954.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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.*3298T>C		3_prime_UTR	Exon 5 of 5	NP_008885.1	Q06730-2
	ZNF33A	NM_001278177.2		c.*3298T>C		3_prime_UTR	Exon 5 of 5	NP_001265106.1
	ZNF33A	NM_001278173.1		c.*3298T>C		3_prime_UTR	Exon 6 of 6	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.*3298T>C		3_prime_UTR	Exon 5 of 5	ENSP00000402467.3	Q06730-2
	ZNF33A	ENST00000458705.6	TSL:1	c.*3298T>C		3_prime_UTR	Exon 5 of 5	ENSP00000387713.2	Q06730-1
	ZNF33A	ENST00000307441.13	TSL:4	c.*3298T>C		3_prime_UTR	Exon 6 of 6	ENSP00000304268.10	A0A0A0MR11

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 3

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		0.47

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: rs1130241; hg19: chr10-38348786;