rs62030476

Variant names:

• chr16-34163122-G-A
• rs62030476
• ENST00000363564.1:n.*12G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000363564.1(RNA5-8SP2):​n.*12G>A variant causes a downstream gene 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 0.50 (5 hom., cov: 84)
  • Exomes 𝑓: 0.36 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RNA5-8SP2 ENST00000363564.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 6 publications found

Genes affected

RNA5-8SP2 (HGNC:41956): (RNA, 5.8S ribosomal pseudogene 2)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000363564.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNA5-8SP2	ENST00000363564.1	TSL:6	n.*12G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76158 AN: 152306 Hom.: 5 Cov.: 84

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.500

GnomAD2 exomes AF: 0.158 AC: 17947 AN: 113816 AF XY: 0.159

Gnomad AFR exome AF: 0.134

Gnomad AMR exome AF: 0.154

Gnomad ASJ exome AF: 0.127

Gnomad EAS exome AF: 0.0896

Gnomad FIN exome AF: 0.201

Gnomad NFE exome AF: 0.187

Gnomad OTH exome AF: 0.121

GnomAD4 exome AF: 0.359 AC: 71007 AN: 197658 Hom.: 0 Cov.: 0 AF XY: 0.351 AC XY: 39450 AN XY: 112522

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.318 AC: 1597 AN: 5024

American (AMR) AF: 0.327 AC: 4590 AN: 14052

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 1324 AN: 5604

East Asian (EAS) AF: 0.324 AC: 2132 AN: 6580

South Asian (SAS) AF: 0.347 AC: 12233 AN: 35304

European-Finnish (FIN) AF: 0.397 AC: 7348 AN: 18516

Middle Eastern (MID) AF: 0.448 AC: 1024 AN: 2286

European-Non Finnish (NFE) AF: 0.369 AC: 37410 AN: 101424

Other (OTH) AF: 0.378 AC: 3349 AN: 8868

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.500 AC: 76217 AN: 152424 Hom.: 5 Cov.: 84 AF XY: 0.500 AC XY: 37274 AN XY: 74544

African (AFR) AF: 0.500 AC: 20810 AN: 41610

American (AMR) AF: 0.500 AC: 7656 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1736 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2597 AN: 5194

South Asian (SAS) AF: 0.500 AC: 2417 AN: 4834

European-Finnish (FIN) AF: 0.500 AC: 5315 AN: 10630

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 34025 AN: 68050

Other (OTH) AF: 0.500 AC: 1058 AN: 2116

Alfa AF: 0.383 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	9.1
DANN	Benign	0.88
PhyloP100		0.43

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs62030476;

hg19: chr16-33965589;

COSMIC: COSV63177590;