10-62427805-C-T

Position:

• chr10-62427805-C-T

Variant summary

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

The ENST00000395255.7(ZNF365):​c.925-31936C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,930 control chromosomes in the GnomAD database, including 22,976 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 0.54 (22976 hom., cov: 31)
• Consequence: ZNF365 ENST00000395255.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

Genes affected

ZNF365 (HGNC:18194): (zinc finger protein 365) This gene encodes a zinc finger protein that may play a role in the repair of DNA damage and maintenance of genome stability. The N-terminal C2H2 zinc finger motif is required to form a protein complex with PARP1 and MRE11, which are known to be involved in the restart of stalled DNA replication forks. A mutation in this gene may be associated with breast cancer susceptibility. [provided by RefSeq, Mar 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF365	NM_199450.3	c.925-31936C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF365	ENST00000395255.7	c.925-31936C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81259 AN: 151812 Hom.: 22965 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.535 AC: 81293 AN: 151930 Hom.: 22976 Cov.: 31 AF XY: 0.533 AC XY: 39547 AN XY: 74236

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.542

Alfa AF: 0.595 Hom.: 22700

Bravo AF: 0.524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7089814; hg19: chr10-64187564;