dbSNP rs41307502: ZNF365:c.*24T>C (chr10-62399813-T-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_014951.3(ZNF365):c.*24T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00939 in 1,596,674 control chromosomes in the GnomAD database, including 86 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 0.0074 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0096 ( 75 hom. )

Consequence

ZNF365
NM_014951.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00100

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]

ZNF365 links:

ENSG00000285837 (HGNC:):

ENSG00000285837 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BS2

High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF365	NM_014951.3 link	c.*24T>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000395254.8	NP_055766.2	Q70YC5-1
ZNF365	NM_199450.3 link	c.924+11237T>C		intron_variant	Intron 3 of 4		NP_955522.1	Q70YC5-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF365	ENST00000395254.8 link	c.*24T>C	3_prime_UTR_variant	Exon 5 of 5	1	NM_014951.3	ENSP00000378674.3	Q70YC5-1
ENSG00000285837	ENST00000647733.1 link	c.924+11237T>C	intron_variant	Intron 3 of 7			ENSP00000502188.1
ZNF365	ENST00000395255.7 link	c.924+11237T>C	intron_variant	Intron 3 of 4	1		ENSP00000378675.3	Q70YC5-2
ZNF365	ENST00000466727.1 link	n.611T>C	non_coding_transcript_exon_variant	Exon 4 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.00741

AC:

1127

AN:

152146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00196

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00347

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.0237

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0103

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00754

AC:

1794

AN:

237980

Hom.:

AF XY:

0.00738

AC XY:

951

AN XY:

128780

show subpopulations

Gnomad AFR exome

AF:

0.00149

Gnomad AMR exome

AF:

0.00231

Gnomad ASJ exome

AF:

0.00486

Gnomad EAS exome

AF:

0.0000570

Gnomad SAS exome

AF:

0.00222

Gnomad FIN exome

AF:

0.0213

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.0107

GnomAD4 exome

AF:

0.00960

AC:

13864

AN:

1444410

Hom.:

Cov.:

AF XY:

0.00931

AC XY:

6664

AN XY:

716086

show subpopulations

Gnomad4 AFR exome

AF:

0.00119

Gnomad4 AMR exome

AF:

0.00248

Gnomad4 ASJ exome

AF:

0.00463

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.00234

Gnomad4 FIN exome

AF:

0.0205

Gnomad4 NFE exome

AF:

0.0107

Gnomad4 OTH exome

AF:

0.00919

GnomAD4 genome

AF:

0.00740

AC:

1126

AN:

152264

Hom.:

Cov.:

AF XY:

0.00791

AC XY:

589

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.00195

Gnomad4 AMR

AF:

0.00346

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00311

Gnomad4 FIN

AF:

0.0237

Gnomad4 NFE

AF:

0.0103

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00838

Hom.:

Bravo

AF:

0.00569

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.0

DANN

Benign

0.62

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over