rs752150

Positions:

• chr19-57684839-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138347.5(ZNF551):​c.82-423G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,636 control chromosomes in the GnomAD database, including 1,986 homozygotes. 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 0.16 (1986 hom., cov: 32)
• Consequence: ZNF551 NM_138347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

ZNF551 (HGNC:25108): (zinc finger protein 551) 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF551	NM_138347.5	c.82-423G>A		intron_variant		ENST00000282296.10	NP_612356.2
ZNF551	NM_001270938.2	c.-3-423G>A		intron_variant			NP_001257867.1
ZNF551	NR_073102.2	n.269-1642G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF551	ENST00000282296.10	c.82-423G>A		intron_variant		1	NM_138347.5	ENSP00000282296	P1
ZNF551	ENST00000601064.1	c.-3-423G>A		intron_variant		1		ENSP00000472674
ZNF551	ENST00000599402.1	n.239-1642G>A		intron_variant, non_coding_transcript_variant		1
ZNF551	ENST00000596085.1	c.34-423G>A		intron_variant		2		ENSP00000472230

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24145 AN: 151518 Hom.: 1990 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.176

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.159 AC: 24174 AN: 151636 Hom.: 1986 Cov.: 32 AF XY: 0.159 AC XY: 11794 AN XY: 74140

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.176

Alfa AF: 0.154 Hom.: 1359

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.79

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: rs752150; hg19: chr19-58196207;