rs200032704

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_001214909.2(ZNF48):​c.286C>A​(p.Arg96Arg) variant causes a synonymous 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.

Frequency

Genomes: not found (cov: 32)

Consequence

ZNF48
NM_001214909.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.701
Variant links:
Genes affected
ZNF48 (HGNC:13114): (zinc finger protein 48) Enables identical protein 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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP7
Synonymous conserved (PhyloP=0.701 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF48NM_001214909.2 linkc.286C>A p.Arg96Arg synonymous_variant Exon 3 of 3 ENST00000613509.2 NP_001201838.1 Q96MX3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF48ENST00000613509.2 linkc.286C>A p.Arg96Arg synonymous_variant Exon 3 of 3 2 NM_001214909.2 ENSP00000480262.1 Q96MX3
ZNF48ENST00000320159.2 linkc.286C>A p.Arg96Arg synonymous_variant Exon 2 of 2 1 ENSP00000324056.2 Q96MX3
ZNF48ENST00000528032.5 linkc.286C>A p.Arg96Arg synonymous_variant Exon 3 of 3 4 ENSP00000435674.1 E9PJ50
ZNF48ENST00000622647 linkc.-84C>A 5_prime_UTR_variant Exon 2 of 2 4 ENSP00000479658.1 A0A087WVT1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
85
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.34
CADD
Benign
9.8
DANN
Benign
0.84
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200032704; hg19: chr16-30408857; COSMIC: COSV100198263; COSMIC: COSV100198263; API