rs7248435

chr19-52613764-T-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001277948.2(ZNF83):c.801A>C(p.Gly267=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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: 𝑓 0.000021 (0 hom., cov: 28)
  • Exomes 𝑓: 0.000034 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF83 NM_001277948.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

Genes affected

ZNF83 (HGNC:13158): (zinc finger protein 83) 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP7: Synonymous conserved (PhyloP=-2.36 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF83	NM_018300.4	c.801A>C	p.Gly267=	synonymous_variant	3/3	ENST00000301096.8
ZNF83	NM_001277948.2	c.801A>C	p.Gly267=	synonymous_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF83	ENST00000301096.8	c.801A>C	p.Gly267=	synonymous_variant	3/3	3	NM_018300.4	P1
	ENST00000702778.1	n.82-7335T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2 AN: 97272 Hom.: 0 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000436

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000444 AC: 8 AN: 180344 Hom.: 1 AF XY: 0.0000404 AC XY: 4 AN XY: 98924

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000126

Gnomad NFE exome AF: 0.0000691

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000340 AC: 33 AN: 969912 Hom.: 1 Cov.: 31 AF XY: 0.0000370 AC XY: 18 AN XY: 486964

Gnomad4 AFR exome AF: 0.0000419

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000905

Gnomad4 SAS exome AF: 0.0000151

Gnomad4 FIN exome AF: 0.000182

Gnomad4 NFE exome AF: 0.0000303

Gnomad4 OTH exome AF: 0.0000252

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000205 AC: 2 AN: 97350 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 46870

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000436

Gnomad4 OTH AF: 0.00

Alfa AF: 0.177 Hom.: 248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	0.20
Dann	Benign	0.37

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: rs7248435; hg19: chr19-53117017; COSMIC: COSV56528530; COSMIC: COSV56528530;