11-63764292-C-A

Variant names:

• chr11-63764292-C-A
• rs1261561168
• NM_001144936.2:c.1331G>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001144936.2(ZFTA):​c.1331G>T​(p.Gly444Val) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G444D) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZFTA NM_001144936.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64
• Publications: 0 publications found

Genes affected

ZFTA (HGNC:28449): (zinc finger translocation associated) Predicted to be involved in negative regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.35364285).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144936.2. 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
	ZFTA	NM_001144936.2	MANE Select	c.1331G>T	p.Gly444Val	missense	Exon 4 of 5	NP_001138408.1	C9JLR9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFTA	ENST00000433688.2	TSL:5 MANE Select	c.1331G>T	p.Gly444Val	missense	Exon 4 of 5	ENSP00000482180.1	C9JLR9
	ZFTA	ENST00000338498.6	TSL:1	c.155-423G>T		intron	N/A	ENSP00000483097.1	A0A087X051
	ZFTA	ENST00000948030.1		c.944G>T	p.Gly315Val	missense	Exon 3 of 4	ENSP00000618089.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1297024 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 639444

African (AFR) AF: 0.00 AC: 0 AN: 25438

American (AMR) AF: 0.00 AC: 0 AN: 22632

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21916

East Asian (EAS) AF: 0.00 AC: 0 AN: 27034

South Asian (SAS) AF: 0.00 AC: 0 AN: 70798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32408

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3928

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1039632

Other (OTH) AF: 0.00 AC: 0 AN: 53238

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.23
CADD	Uncertain	26
DANN	Benign	0.97
DEOGEN2	Benign	0.032	T
FATHMM_MKL	Benign	0.67	D
LIST_S2	Benign	0.80	T
MetaRNN	Benign	0.35	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		2.6
Sift4G	Benign	0.31	T
Polyphen		1.0	D
Vest4		0.39
MVP		0.15
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.6
Varity_R		0.33
gMVP		0.47
Mutation Taster		=98/2	polymorphism

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: rs1261561168; hg19: chr11-63531764;