rs200032704

Variant names:

• chr16-30397536-C-A
• rs200032704
• NM_001214909.2:c.286C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-30397536-C-A
• chr16-30397536-C-G
• chr16-30397536-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701

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]

ACMG classification

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
ZNF48	NM_001214909.2	c.286C>A	p.Arg96Arg	synonymous_variant	Exon 3 of 3	ENST00000613509.2	NP_001201838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF48	ENST00000613509.2	c.286C>A	p.Arg96Arg	synonymous_variant	Exon 3 of 3	2	NM_001214909.2	ENSP00000480262.1
ZNF48	ENST00000320159.2	c.286C>A	p.Arg96Arg	synonymous_variant	Exon 2 of 2	1		ENSP00000324056.2
ZNF48	ENST00000528032.5	c.286C>A	p.Arg96Arg	synonymous_variant	Exon 3 of 3	4		ENSP00000435674.1
ZNF48	ENST00000622647	c.-84C>A		5_prime_UTR_variant	Exon 2 of 2	4		ENSP00000479658.1

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

Other links and lift over

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