rs16848861

Variant names:

• chr1-236981614-A-G
• rs16848861
• ENST00000450819.1:n.276A>G

Variant summary

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

The ENST00000450819.1(RPL35P1):​n.276A>G 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 0.028 in 1,331,980 control chromosomes in the GnomAD database, including 2,653 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 0.070 (844 hom., cov: 33)
  • Exomes 𝑓: 0.023 (1809 hom.)
• Consequence: RPL35P1 ENST00000450819.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 3 publications found

Genes affected

RPL35P1 (HGNC:36695): (ribosomal protein L35 pseudogene 1)

ENSG00000302268 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450819.1. 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
	RPL35P1	ENST00000450819.1	TSL:6	n.276A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000302268	ENST00000785366.1		n.299-772A>G		intron	N/A
	ENSG00000302268	ENST00000785367.1		n.173-772A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10556 AN: 152210 Hom.: 832 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00362

Gnomad OTH AF: 0.0587

GnomAD4 exome AF: 0.0226 AC: 26669 AN: 1179654 Hom.: 1809 Cov.: 20 AF XY: 0.0232 AC XY: 13890 AN XY: 599998

African (AFR) AF: 0.196 AC: 5665 AN: 28830

American (AMR) AF: 0.0155 AC: 684 AN: 44156

Ashkenazi Jewish (ASJ) AF: 0.00468 AC: 114 AN: 24368

East Asian (EAS) AF: 0.197 AC: 7585 AN: 38406

South Asian (SAS) AF: 0.0603 AC: 4853 AN: 80484

European-Finnish (FIN) AF: 0.0688 AC: 3619 AN: 52568

Middle Eastern (MID) AF: 0.0250 AC: 90 AN: 3604

European-Non Finnish (NFE) AF: 0.00262 AC: 2247 AN: 856232

Other (OTH) AF: 0.0355 AC: 1812 AN: 51006

GnomAD4 genome AF: 0.0697 AC: 10615 AN: 152326 Hom.: 844 Cov.: 33 AF XY: 0.0721 AC XY: 5374 AN XY: 74492

African (AFR) AF: 0.186 AC: 7728 AN: 41568

American (AMR) AF: 0.0329 AC: 503 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.162 AC: 838 AN: 5182

South Asian (SAS) AF: 0.0677 AC: 327 AN: 4830

European-Finnish (FIN) AF: 0.0760 AC: 807 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00363 AC: 247 AN: 68034

Other (OTH) AF: 0.0615 AC: 130 AN: 2114

Alfa AF: 0.466 Hom.: 6671

Bravo AF: 0.0724

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.5
DANN	Benign	0.099
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs16848861; hg19: chr1-237144914;