chr2-36299293-T-G

Variant names:

• chr2-36299293-T-G
• rs1863080
• ENST00000427200.1:n.*95A>C

Variant summary

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

The ENST00000427200.1(RPL21P36):​n.*95A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 182,672 control chromosomes in the GnomAD database, including 4,179 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 0.19 (3695 hom., cov: 32)
  • Exomes 𝑓: 0.13 (484 hom.)
• Consequence: RPL21P36 ENST00000427200.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 5 publications found

Genes affected

RPL21P36 (HGNC:36128): (ribosomal protein L21 pseudogene 36)

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 (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427200.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL21P36	ENST00000427200.1	TSL:6	n.*95A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28750 AN: 151804 Hom.: 3686 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0941

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.0967

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.132 AC: 4059 AN: 30750 Hom.: 484 AF XY: 0.144 AC XY: 2479 AN XY: 17210

African (AFR) AF: 0.301 AC: 161 AN: 534

American (AMR) AF: 0.274 AC: 347 AN: 1268

Ashkenazi Jewish (ASJ) AF: 0.0760 AC: 52 AN: 684

East Asian (EAS) AF: 0.313 AC: 315 AN: 1006

South Asian (SAS) AF: 0.338 AC: 1240 AN: 3672

European-Finnish (FIN) AF: 0.0815 AC: 104 AN: 1276

Middle Eastern (MID) AF: 0.138 AC: 18 AN: 130

European-Non Finnish (NFE) AF: 0.0789 AC: 1617 AN: 20498

Other (OTH) AF: 0.122 AC: 205 AN: 1682

GnomAD4 genome AF: 0.190 AC: 28799 AN: 151922 Hom.: 3695 Cov.: 32 AF XY: 0.195 AC XY: 14455 AN XY: 74266

African (AFR) AF: 0.323 AC: 13369 AN: 41392

American (AMR) AF: 0.242 AC: 3698 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0941 AC: 326 AN: 3466

East Asian (EAS) AF: 0.352 AC: 1812 AN: 5148

South Asian (SAS) AF: 0.365 AC: 1752 AN: 4802

European-Finnish (FIN) AF: 0.0967 AC: 1022 AN: 10566

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.0928 AC: 6308 AN: 67956

Other (OTH) AF: 0.170 AC: 359 AN: 2116

Alfa AF: 0.140 Hom.: 1315

Bravo AF: 0.204

Asia WGS AF: 0.335 AC: 1163 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	1.0
DANN	Benign	0.30
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1863080; hg19: chr2-36526436;