rs2008514

Variant names:

• chr16-28814284-G-A
• rs2008514
• ENST00000469929.1:n.390C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-28814284-G-A
• chr16-28814284-G-C
• chr16-28814284-G-T

Variant summary

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

The ENST00000469929.1(ENSG00000240634):​n.390C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 305,744 control chromosomes in the GnomAD database, including 19,823 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 0.35 (9733 hom., cov: 32)
  • Exomes 𝑓: 0.35 (10090 hom.)
• Consequence: ENSG00000240634 ENST00000469929.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34
• Publications: 44 publications found

Genes affected

ENSG00000240634 (HGNC:):

RPS15AP33 (HGNC:36178):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS15AP33		n.28814284G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000240634	ENST00000469929.1	n.390C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000251417	ENST00000507031.3	n.271-1852G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52344 AN: 151644 Hom.: 9702 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.355 AC: 54642 AN: 153984 Hom.: 10090 Cov.: 0 AF XY: 0.351 AC XY: 28992 AN XY: 82482

African (AFR) AF: 0.272 AC: 920 AN: 3382

American (AMR) AF: 0.474 AC: 2578 AN: 5440

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 1383 AN: 4876

East Asian (EAS) AF: 0.131 AC: 1247 AN: 9512

South Asian (SAS) AF: 0.250 AC: 3108 AN: 12438

European-Finnish (FIN) AF: 0.393 AC: 4523 AN: 11496

Middle Eastern (MID) AF: 0.242 AC: 141 AN: 582

European-Non Finnish (NFE) AF: 0.387 AC: 37625 AN: 97334

Other (OTH) AF: 0.349 AC: 3117 AN: 8924

GnomAD4 genome AF: 0.346 AC: 52438 AN: 151760 Hom.: 9733 Cov.: 32 AF XY: 0.343 AC XY: 25460 AN XY: 74128

African (AFR) AF: 0.271 AC: 11221 AN: 41404

American (AMR) AF: 0.410 AC: 6240 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3470

East Asian (EAS) AF: 0.120 AC: 618 AN: 5166

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4820

European-Finnish (FIN) AF: 0.421 AC: 4407 AN: 10468

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26914 AN: 67910

Other (OTH) AF: 0.321 AC: 676 AN: 2104

Alfa AF: 0.375 Hom.: 31136

Bravo AF: 0.344

Asia WGS AF: 0.276 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.62
DANN	Benign	0.63
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs2008514; hg19: chr16-28825605;