rs752150

Variant names:

• chr19-57684839-G-A
• rs752150
• NM_138347.5:c.82-423G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

ENSG00000269026 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138347.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF551	NM_138347.5	MANE Select	c.82-423G>A		intron	N/A	NP_612356.2	Q7Z340-1
	ZNF551	NM_001270938.2		c.-3-423G>A		intron	N/A	NP_001257867.1
	ZNF551	NR_073102.2		n.269-1642G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF551	ENST00000282296.10	TSL:1 MANE Select	c.82-423G>A		intron	N/A	ENSP00000282296.5	Q7Z340-1
	ZNF551	ENST00000601064.1	TSL:1	c.-3-423G>A		intron	N/A	ENSP00000472674.1	M0R2M4
	ENSG00000269026	ENST00000594684.1	TSL:1	c.33+2595G>A		intron	N/A	ENSP00000472160.1	M0R1X1

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

African (AFR) AF: 0.156 AC: 6444 AN: 41434

American (AMR) AF: 0.154 AC: 2338 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1297 AN: 5142

South Asian (SAS) AF: 0.0826 AC: 398 AN: 4820

European-Finnish (FIN) AF: 0.156 AC: 1650 AN: 10578

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10723 AN: 67664

Other (OTH) AF: 0.176 AC: 372 AN: 2108

Alfa AF: 0.158 Hom.: 4960

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.79
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs752150; hg19: chr19-58196207;