22-42512119-G-C

Position:

• chr22-42512119-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_015703.5(RRP7A):​c.*791C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00019 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RRP7A NM_015703.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.749

Genes affected

RRP7A (HGNC:24286): (ribosomal RNA processing 7 homolog A) Enables RNA binding activity. Predicted to be involved in rRNA processing and ribosomal small subunit assembly. Predicted to act upstream of or within blastocyst formation. Predicted to be located in nucleoplasm. Predicted to be part of CURI complex and UTP-C complex. Implicated in primary autosomal recessive microcephaly. [provided by Alliance of Genome Resources, Apr 2022]

SERHL (HGNC:14408): (serine hydrolase like (pseudogene)) Predicted to enable hydrolase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RRP7A	NM_015703.5	c.*791C>G		3_prime_UTR_variant	7/7	ENST00000323013.7	NP_056518.2
SERHL	NR_027786.1	n.916G>C		splice_region_variant, non_coding_transcript_exon_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RRP7A	ENST00000323013.7	c.*791C>G		3_prime_UTR_variant	7/7	1	NM_015703.5	ENSP00000321449	P1
SERHL	ENST00000359906.7	n.942G>C		splice_region_variant, non_coding_transcript_exon_variant	11/11	1
SERHL	ENST00000642172.1	n.712G>C		splice_region_variant, non_coding_transcript_exon_variant	10/10

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 147464 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000193 AC: 161 AN: 835030 Hom.: 0 Cov.: 24 AF XY: 0.000205 AC XY: 89 AN XY: 433886

Gnomad4 AFR exome AF: 0.000146

Gnomad4 AMR exome AF: 0.0000264

Gnomad4 ASJ exome AF: 0.000324

Gnomad4 EAS exome AF: 0.000259

Gnomad4 SAS exome AF: 0.0000413

Gnomad4 FIN exome AF: 0.0000664

Gnomad4 NFE exome AF: 0.000225

Gnomad4 OTH exome AF: 0.000219

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 147584 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 71864

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.6
DANN	Benign	0.68

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-42908125;