rs1133146

Variant summary

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

The NM_024733.5(ZNF665):​c.*1046C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,062 control chromosomes in the GnomAD database, including 22,956 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 0.52 ( 22954 hom., cov: 32)
Exomes 𝑓: 0.67 ( 2 hom. )

Consequence

ZNF665
NM_024733.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88
Variant links:
Genes affected
ZNF665 (HGNC:25885): (zinc finger protein 665) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF665NM_024733.5 linkuse as main transcriptc.*1046C>T 3_prime_UTR_variant 4/4 ENST00000396424.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF665ENST00000396424.5 linkuse as main transcriptc.*1046C>T 3_prime_UTR_variant 4/42 NM_024733.5 P1
ENST00000600257.1 linkuse as main transcriptn.203G>A non_coding_transcript_exon_variant 2/23
ZNF665ENST00000596564.1 linkuse as main transcriptn.50+443C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.516
AC:
78459
AN:
151940
Hom.:
22942
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.229
Gnomad AMI
AF:
0.629
Gnomad AMR
AF:
0.615
Gnomad ASJ
AF:
0.507
Gnomad EAS
AF:
0.655
Gnomad SAS
AF:
0.716
Gnomad FIN
AF:
0.668
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.620
Gnomad OTH
AF:
0.519
GnomAD4 exome
AF:
0.667
AC:
4
AN:
6
Hom.:
2
Cov.:
0
AF XY:
0.667
AC XY:
4
AN XY:
6
show subpopulations
Gnomad4 NFE exome
AF:
1.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.516
AC:
78500
AN:
152056
Hom.:
22954
Cov.:
32
AF XY:
0.524
AC XY:
38951
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.229
Gnomad4 AMR
AF:
0.616
Gnomad4 ASJ
AF:
0.507
Gnomad4 EAS
AF:
0.656
Gnomad4 SAS
AF:
0.716
Gnomad4 FIN
AF:
0.668
Gnomad4 NFE
AF:
0.620
Gnomad4 OTH
AF:
0.520
Alfa
AF:
0.591
Hom.:
26848
Bravo
AF:
0.497
Asia WGS
AF:
0.652
AC:
2268
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.7
DANN
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs1133146; hg19: chr19-53666660; API