rs142150770

Variant names:

• chr19-57473600-C-G
• NM_001144068.2:c.1021G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-57473600-C-G
• chr19-57473600-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001144068.2(ZNF772):​c.1021G>C​(p.Glu341Gln) 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 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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. E341K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: ZNF772 NM_001144068.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

ZNF772 (HGNC:33106): (zinc finger protein 772) Predicted to enable DNA-binding transcription factor 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]

ENSG00000268163 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19888812).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF772	NM_001144068.2	c.1021G>C	p.Glu341Gln	missense_variant	Exon 4 of 4	ENST00000356584.8	NP_001137540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF772	ENST00000356584.8	c.1021G>C	p.Glu341Gln	missense_variant	Exon 4 of 4	2	NM_001144068.2	ENSP00000348992.3
ENSG00000268163	ENST00000596831.1	c.199+2060G>C		intron_variant	Intron 3 of 5	2		ENSP00000470969.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461868 Hom.: 0 Cov.: 41 AF XY: 0.00 AC XY: 0 AN XY: 727224

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

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	Benign	0.20
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	20
DANN	Uncertain	1.0
DEOGEN2	Benign	0.085	T;.;.;.;.
Eigen	Benign	-0.033
Eigen_PC	Benign	-0.071
FATHMM_MKL	Benign	0.15	N
LIST_S2	Benign	0.21	T;T;T;T;T
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.20	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.35	N;.;.;.;.
PrimateAI	Uncertain	0.53	T
PROVEAN	Uncertain	-2.8	D;D;D;.;.
REVEL	Benign	0.12
Sift	Uncertain	0.015	D;D;D;.;.
Sift4G	Uncertain	0.015	D;D;D;D;D
Polyphen		1.0	D;P;.;.;.
Vest4		0.17
MutPred		0.52		Loss of ubiquitination at K385 (P = 0.0352);.;.;.;.;
MVP		0.46
MPC		0.80
ClinPred		0.83	D
GERP RS		4.1
Varity_R		0.27
gMVP		0.15

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: chr19-57984968;