rs10276062

Variant names:

• chr7-112268107-T-C
• rs10276062
• NM_021994.3:c.92-18766T>C

Variant summary

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

The NM_021994.3(ZNF277):​c.92-18766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0576 in 152,160 control chromosomes in the GnomAD database, including 672 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 0.058 (672 hom., cov: 32)
• Consequence: ZNF277 NM_021994.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 1 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF277	NM_021994.3	c.92-18766T>C		intron_variant	Intron 1 of 11	ENST00000361822.8	NP_068834.2
ZNF277	XM_011515768.4	c.-139-18770T>C		intron_variant	Intron 1 of 11		XP_011514070.1
ZNF277	XM_017011720.3	c.-170-18770T>C		intron_variant	Intron 1 of 10		XP_016867209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF277	ENST00000361822.8	c.92-18766T>C		intron_variant	Intron 1 of 11	1	NM_021994.3	ENSP00000354501.3

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8727 AN: 152042 Hom.: 666 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.00623

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00978

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0576 AC: 8757 AN: 152160 Hom.: 672 Cov.: 32 AF XY: 0.0552 AC XY: 4108 AN XY: 74412

African (AFR) AF: 0.176 AC: 7323 AN: 41490

American (AMR) AF: 0.0261 AC: 399 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3466

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0243 AC: 117 AN: 4822

European-Finnish (FIN) AF: 0.00623 AC: 66 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00976 AC: 664 AN: 68016

Other (OTH) AF: 0.0488 AC: 103 AN: 2112

Alfa AF: 0.0417 Hom.: 69

Bravo AF: 0.0634

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		-0.084
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: rs10276062; hg19: chr7-111908162;