rs10487289

chr7-112268871-A-G

Variant summary

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

The NM_021994.3(ZNF277):c.92-18002A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,224 control chromosomes in the GnomAD database, including 641 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 0.056 (641 hom., cov: 32)
• Consequence: ZNF277 NM_021994.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696

Genes affected

ZNF277 (HGNC:13070): (zinc finger protein 277) Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and metal ion binding activity. Predicted to act upstream of or within cellular response to hydrogen peroxide and regulation of cellular senescence. 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF277	NM_021994.3	c.92-18002A>G		intron_variant		ENST00000361822.8
ZNF277	XM_011515768.4	c.-139-18006A>G		intron_variant
ZNF277	XM_017011720.3	c.-170-18006A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF277	ENST00000361822.8	c.92-18002A>G		intron_variant		1	NM_021994.3	P1

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8532 AN: 152106 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00972

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0562 AC: 8561 AN: 152224 Hom.: 641 Cov.: 32 AF XY: 0.0541 AC XY: 4029 AN XY: 74426

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.00603

Gnomad4 NFE AF: 0.00971

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0381 Hom.: 72

Bravo AF: 0.0621

Asia WGS AF: 0.0200 AC: 70 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.6
Dann	Benign	0.82

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: rs10487289; hg19: chr7-111908926;