GeneBe

rs521678

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_032193.4(RNASEH2C):​c.*1527A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RNASEH2C
NM_032193.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.452

Publications

11 publications found
Variant links:
Genes affected
RNASEH2C (HGNC:24116): (ribonuclease H2 subunit C) This gene encodes a ribonuclease H subunit that can cleave ribonucleotides from RNA:DNA duplexes. Mutations in this gene cause Aicardi-Goutieres syndrome-3, a disease that causes severe neurologic dysfunction. A pseudogene for this gene has been identified on chromosome Y, near the sex determining region Y (SRY) gene. [provided by RefSeq, Jul 2008]
KAT5 (HGNC:5275): (lysine acetyltransferase 5) The protein encoded by this gene belongs to the MYST family of histone acetyl transferases (HATs) and was originally isolated as an HIV-1 TAT-interactive protein. HATs play important roles in regulating chromatin remodeling, transcription and other nuclear processes by acetylating histone and nonhistone proteins. This protein is a histone acetylase that has a role in DNA repair and apoptosis and is thought to play an important role in signal transduction. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
KAT5 Gene-Disease associations (from GenCC):
  • neurodevelopmental disorder with dysmorphic facies, sleep disturbance, and brain abnormalities
    Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RNASEH2CNM_032193.4 linkc.*1527A>T 3_prime_UTR_variant Exon 4 of 4 ENST00000308418.10 NP_115569.2
KAT5NM_182710.3 linkc.1265-334T>A intron_variant Intron 10 of 12 ENST00000341318.9 NP_874369.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RNASEH2CENST00000308418.10 linkc.*1527A>T 3_prime_UTR_variant Exon 4 of 4 1 NM_032193.4 ENSP00000308193.5
KAT5ENST00000341318.9 linkc.1265-334T>A intron_variant Intron 10 of 12 1 NM_182710.3 ENSP00000340330.4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
79464
Hom.:
0
Cov.:
2
AF XY:
0.00
AC XY:
0
AN XY:
41254
African (AFR)
AF:
0.00
AC:
0
AN:
2758
American (AMR)
AF:
0.00
AC:
0
AN:
4612
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2532
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5450
South Asian (SAS)
AF:
0.00
AC:
0
AN:
6942
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3262
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
296
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
49008
Other (OTH)
AF:
0.00
AC:
0
AN:
4604
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.3
DANN
Benign
0.71
PhyloP100
-0.45
PromoterAI
-0.0036
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs521678; hg19: chr11-65485727; API