chr10-62427805-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.310
Variant links:
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]

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ACMG classification

Classification made for transcript

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 Protein UniProt
ZNF365NM_199450.3 linkuse as main transcriptc.925-31936C>T intron_variant NP_955522.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF365ENST00000395255.7 linkuse as main transcriptc.925-31936C>T intron_variant 1 ENSP00000378675 Q70YC5-2

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7089814; hg19: chr10-64187564; API