rs1780076589

Variant names:

• chr7-6691983-G-A
• NM_016265.4:c.959C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-6691983-G-A
• chr7-6691983-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_016265.4(ZNF12):​c.959C>T​(p.Thr320Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. T320K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: ZNF12 NM_016265.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49

Genes affected

ZNF12 (HGNC:12902): (zinc finger protein 12) This gene is a member of the krueppel C2H2-type zinc-finger protein family and encodes a protein with eight C2H2-type zinc fingers and a KRAB domain. This nuclear protein is involved in developmental control of gene expression. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ENSG00000228010 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.27573705).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF12	NM_016265.4	c.959C>T	p.Thr320Ile	missense_variant	Exon 5 of 5	ENST00000405858.6	NP_057349.2
ZNF12	NM_006956.3	c.845C>T	p.Thr282Ile	missense_variant	Exon 6 of 6		NP_008887.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF12	ENST00000405858.6	c.959C>T	p.Thr320Ile	missense_variant	Exon 5 of 5	1	NM_016265.4	ENSP00000385939.1
ZNF12	ENST00000404360.5	c.737C>T	p.Thr246Ile	missense_variant	Exon 5 of 5	1		ENSP00000384405.1
ZNF12	ENST00000342651.9	c.845C>T	p.Thr282Ile	missense_variant	Exon 6 of 6	2		ENSP00000344745.5
ENSG00000228010	ENST00000366167.2	n.136-16318G>A		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461862 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727230

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.20	.;T;.
Eigen	Benign	-0.026
Eigen_PC	Benign	-0.086
FATHMM_MKL	Benign	0.0038	N
LIST_S2	Benign	0.18	T;T;T
M_CAP	Benign	0.0090	T
MetaRNN	Benign	0.28	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	2.0	.;M;.
PrimateAI	Uncertain	0.67	T
PROVEAN	Uncertain	-4.3	D;D;D
REVEL	Benign	0.076
Sift	Uncertain	0.0040	D;D;D
Sift4G	Uncertain	0.011	D;D;D
Polyphen		0.76, 0.93	.;P;P
Vest4		0.40
MutPred		0.44		.;Loss of disorder (P = 0.0367);.;
MVP		0.31
MPC		0.77
ClinPred		0.98	D
GERP RS		1.3
Varity_R		0.14
gMVP		0.079

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-6731614;