20-5013816-G-T

Variant names:

• chr20-5013816-G-T
• rs6053034
• ENST00000435457.1:n.-92C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435457.1(RPS21P7):​n.-92C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,032 control chromosomes in the GnomAD database, including 8,259 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 0.27 (8259 hom., cov: 31)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: RPS21P7 ENST00000435457.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 2 publications found

Genes affected

RPS21P7 (HGNC:35577):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435457.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS21P7	ENST00000435457.1	TSL:6	n.-92C>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41608 AN: 151802 Hom.: 8242 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.134 AC: 15 AN: 112 Hom.: 0 AF XY: 0.111 AC XY: 10 AN XY: 90

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.125 AC: 1 AN: 8

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.144 AC: 13 AN: 90

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.274 AC: 41651 AN: 151920 Hom.: 8259 Cov.: 31 AF XY: 0.270 AC XY: 20042 AN XY: 74238

African (AFR) AF: 0.567 AC: 23470 AN: 41388

American (AMR) AF: 0.197 AC: 2996 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3466

East Asian (EAS) AF: 0.0156 AC: 81 AN: 5178

South Asian (SAS) AF: 0.156 AC: 750 AN: 4808

European-Finnish (FIN) AF: 0.152 AC: 1610 AN: 10570

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11375 AN: 67968

Other (OTH) AF: 0.256 AC: 539 AN: 2102

Alfa AF: 0.187 Hom.: 3071

Bravo AF: 0.289

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs6053034; hg19: chr20-4994462;