rs1542039

chr19-56473006-T-Cchr19-56473006-T-G

Variant summary

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

The NM_001321356.2(ZNF667):c.-548-819A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,144 control chromosomes in the GnomAD database, including 11,692 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 0.38 (11692 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ZNF667 NM_001321356.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844

Genes affected

ZNF667 (HGNC:28854): (zinc finger protein 667) Predicted to enable DNA-binding transcription factor activity 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF667	NM_001321356.2	c.-548-819A>G		intron_variant		ENST00000504904.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF667	ENST00000504904.8	c.-548-819A>G		intron_variant		2	NM_001321356.2	P1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58058 AN: 152024 Hom.: 11690 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.382 AC: 58071 AN: 152142 Hom.: 11692 Cov.: 32 AF XY: 0.377 AC XY: 28058 AN XY: 74384

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.403

Alfa AF: 0.443 Hom.: 26470

Bravo AF: 0.374

Asia WGS AF: 0.239 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.74

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: rs1542039; hg19: chr19-56984375;