11-65718007-G-A

Variant names:

• chr11-65718007-G-A
• rs4645936
• NM_032193.4:c.*1776C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_032193.4(RNASEH2C):​c.*1776C>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 0.0385 in 153,796 control chromosomes in the GnomAD database, including 200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.039 (199 hom., cov: 32)
  • Exomes 𝑓: 0.034 (1 hom.)
• Consequence: RNASEH2C NM_032193.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.596

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 11-65718007-G-A is Benign according to our data. Variant chr11-65718007-G-A is described in ClinVar as [Benign]. Clinvar id is 305328.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0385 (5867/152230) while in subpopulation NFE AF= 0.0507 (3446/68010). AF 95% confidence interval is 0.0493. There are 199 homozygotes in gnomad4. There are 3149 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 199 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNASEH2C	NM_032193.4	c.*1776C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000308418.10	NP_115569.2
KAT5	NM_182710.3	c.1265-583G>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
RNASEH2C	ENST00000308418	c.*1776C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_032193.4	ENSP00000308193.5
KAT5	ENST00000341318.9	c.1265-583G>A		intron_variant	Intron 10 of 12	1	NM_182710.3	ENSP00000340330.4

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5868 AN: 152112 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.00842

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0205

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.0292

GnomAD4 exome AF: 0.0338 AC: 53 AN: 1566 Hom.: 1 Cov.: 0 AF XY: 0.0340 AC XY: 28 AN XY: 824

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0438

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0385 AC: 5867 AN: 152230 Hom.: 199 Cov.: 32 AF XY: 0.0423 AC XY: 3149 AN XY: 74418

Gnomad4 AFR AF: 0.00840

Gnomad4 AMR AF: 0.0204

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.0507

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0426 Hom.: 28

Bravo AF: 0.0275

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Aicardi-Goutieres syndrome 3 Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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

Other links and lift over

dbSNP: rs4645936; hg19: chr11-65485478;