19-57398923-T-G

Variant names:

• chr19-57398923-T-G
• NM_001172773.2:c.672T>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_001172773.2(ZNF548):​c.672T>G​(p.Phe224Leu) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF548 NM_001172773.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.37

Genes affected

ZNF548 (HGNC:26561): (zinc finger protein 548) 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]

ENSG00000269533 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.027445197).
• BP6: Variant 19-57398923-T-G is Benign according to our data. Variant chr19-57398923-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2278523.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF548	NM_001172773.2	c.672T>G	p.Phe224Leu	missense_variant	Exon 4 of 4	ENST00000336128.12	NP_001166244.1
ZNF548	NM_152909.4	c.636T>G	p.Phe212Leu	missense_variant	Exon 3 of 3		NP_690873.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF548	ENST00000336128.12	c.672T>G	p.Phe224Leu	missense_variant	Exon 4 of 4	2	NM_001172773.2	ENSP00000337555.6
ENSG00000269533	ENST00000596400.1	c.51+4700T>G		intron_variant	Intron 2 of 3	4		ENSP00000472277.1
ENSG00000268533	ENST00000597410.1	c.39+4700T>G		intron_variant	Intron 1 of 2	3		ENSP00000472152.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 16, 2022

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.2
DANN	Benign	0.49
DEOGEN2	Benign	0.0088	T;.
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.082	N
LIST_S2	Benign	0.0046	T;T
M_CAP	Benign	0.0014	T
MetaRNN	Benign	0.027	T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	-1.3	N;.
PrimateAI	Benign	0.31	T
PROVEAN	Benign	2.5	N;N
REVEL	Benign	0.089
Sift	Benign	1.0	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;B
Vest4		0.020
MutPred		0.57		Loss of ubiquitination at K217 (P = 0.0777);.;
MVP		0.085
MPC		0.17
ClinPred		0.046	T
GERP RS		0.58
Varity_R		0.029
gMVP		0.081

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: chr19-57910291;