12-51888771-G-T

Variant names:

• chr12-51888771-G-T
• ENST00000340970.8:c.-53G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001304459.2(ANKRD33):​c.-53G>T variant causes a 5 prime UTR premature start codon gain 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ANKRD33 NM_001304459.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.178
• Publications: 0 publications found

Genes affected

ANKRD33 (HGNC:13788): (ankyrin repeat domain 33) Predicted to be involved in negative regulation of transcription by RNA polymerase II and negative regulation of transcription regulatory region DNA binding activity. Predicted to act upstream of or within skeletal muscle cell differentiation. Predicted to be located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07399258).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304459.2. 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
	ANKRD33	NM_182608.4	MANE Select	c.349G>T	p.Gly117Cys	missense	Exon 2 of 5	NP_872414.3
	ANKRD33	NM_001304459.2		c.-53G>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 6	NP_001291388.1
	ANKRD33	NM_001130015.2		c.-53G>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 6	NP_001123487.1	Q7Z3H0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD33	ENST00000340970.8	TSL:1	c.-53G>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 6	ENSP00000344690.4	Q7Z3H0-1
	ANKRD33	ENST00000301190.11	TSL:2 MANE Select	c.349G>T	p.Gly117Cys	missense	Exon 2 of 5	ENSP00000301190.6	Q7Z3H0-2
	ANKRD33	ENST00000340970.8	TSL:1	c.-53G>T		5_prime_UTR	Exon 2 of 6	ENSP00000344690.4	Q7Z3H0-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.97
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.86
FATHMM_MKL	Benign	0.10	N
LIST_S2	Benign	0.31	T
M_CAP	Benign	0.057	D
MetaRNN	Benign	0.074	T
MetaSVM	Benign	-0.96	T
PhyloP100		0.18
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-0.99	N
REVEL	Benign	0.14
Sift	Benign	0.056	T
Sift4G	Benign	0.061	T
Vest4		0.25
MutPred		0.33		Loss of relative solvent accessibility (P = 0.0186)
MVP		0.18
MPC		0.34
ClinPred		0.55	D
GERP RS		0.22
Varity_R		0.13
gMVP		0.32
Mutation Taster		=95/5	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

hg19: chr12-52282555;