chr19-53247262-G-A

Variant names:

• chr19-53247262-G-A
• rs8100275
• NM_182609.4:c.16-3365C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182609.4(ZNF677):​c.16-3365C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,866 control chromosomes in the GnomAD database, including 8,750 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 0.31 (8750 hom., cov: 31)
• Consequence: ZNF677 NM_182609.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 4 publications found

Genes affected

ZNF677 (HGNC:28730): (zinc finger protein 677) 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]

ENSG00000291131 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182609.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF677	NM_182609.4	MANE Select	c.16-3365C>T		intron	N/A	NP_872415.1
	ZNF677	NR_169728.1		n.393C>T		non_coding_transcript_exon	Exon 4 of 6
	ZNF677	NM_001317998.2		c.16-3365C>T		intron	N/A	NP_001304927.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF677	ENST00000598513.6	TSL:1 MANE Select	c.16-3365C>T		intron	N/A	ENSP00000469391.1
	ZNF677	ENST00000594517.5	TSL:1	c.16-3365C>T		intron	N/A	ENSP00000472416.1
	ZNF677	ENST00000598806.5	TSL:1	c.16-3365C>T		intron	N/A	ENSP00000471071.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47660 AN: 151748 Hom.: 8728 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.314 AC: 47728 AN: 151866 Hom.: 8750 Cov.: 31 AF XY: 0.308 AC XY: 22837 AN XY: 74202

African (AFR) AF: 0.502 AC: 20773 AN: 41380

American (AMR) AF: 0.264 AC: 4032 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3468

East Asian (EAS) AF: 0.0495 AC: 256 AN: 5172

South Asian (SAS) AF: 0.252 AC: 1211 AN: 4802

European-Finnish (FIN) AF: 0.217 AC: 2287 AN: 10526

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17309 AN: 67948

Other (OTH) AF: 0.327 AC: 687 AN: 2104

Alfa AF: 0.308 Hom.: 1269

Bravo AF: 0.323

Asia WGS AF: 0.163 AC: 570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.69
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8100275; hg19: chr19-53750515;