2-218841971-C-T

Variant names:

• chr2-218841971-C-T
• rs691574
• ENST00000456160.1:n.373C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000456160.1(RPL23AP31):​n.373C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.172 in 645,170 control chromosomes in the GnomAD database, including 10,874 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 0.15 (2082 hom., cov: 32)
  • Exomes 𝑓: 0.18 (8792 hom.)
• Consequence: RPL23AP31 ENST00000456160.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.71
• Publications: 3 publications found

Genes affected

RPL23AP31 (HGNC:35777): (ribosomal protein L23a pseudogene 31)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456160.1. 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
	RPL23AP31	ENST00000456160.1	TSL:6	n.373C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22572 AN: 152066 Hom.: 2075 Cov.: 32

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.179 AC: 88085 AN: 492986 Hom.: 8792 Cov.: 0 AF XY: 0.179 AC XY: 49214 AN XY: 274446

African (AFR) AF: 0.0692 AC: 1004 AN: 14506

American (AMR) AF: 0.171 AC: 6883 AN: 40164

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 3957 AN: 16732

East Asian (EAS) AF: 0.388 AC: 9397 AN: 24206

South Asian (SAS) AF: 0.178 AC: 12250 AN: 68636

European-Finnish (FIN) AF: 0.106 AC: 2756 AN: 25894

Middle Eastern (MID) AF: 0.171 AC: 326 AN: 1904

European-Non Finnish (NFE) AF: 0.171 AC: 46991 AN: 275594

Other (OTH) AF: 0.178 AC: 4521 AN: 25350

GnomAD4 genome AF: 0.148 AC: 22598 AN: 152184 Hom.: 2082 Cov.: 32 AF XY: 0.148 AC XY: 11013 AN XY: 74398

African (AFR) AF: 0.0679 AC: 2819 AN: 41524

American (AMR) AF: 0.171 AC: 2616 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2126 AN: 5164

South Asian (SAS) AF: 0.174 AC: 838 AN: 4816

European-Finnish (FIN) AF: 0.115 AC: 1220 AN: 10596

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11610 AN: 68012

Other (OTH) AF: 0.151 AC: 318 AN: 2110

Alfa AF: 0.170 Hom.: 771

Bravo AF: 0.150

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	4.2
DANN	Benign	0.69
PhyloP100		5.7

Splicing

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

Other links and lift over

dbSNP: rs691574; hg19: chr2-219706694;