rs16848861

Positions:

• chr1-236981614-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC124904563 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904563	XR_007066964.1	n.270-772A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL35P1	ENST00000450819.1	n.276A>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.196

Gnomad4 AMR exome AF: 0.0155

Gnomad4 ASJ exome AF: 0.00468

Gnomad4 EAS exome AF: 0.197

Gnomad4 SAS exome AF: 0.0603

Gnomad4 FIN exome AF: 0.0688

Gnomad4 NFE exome AF: 0.00262

Gnomad4 OTH exome AF: 0.0355

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

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0677

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.00363

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0433 Hom.: 48

Bravo AF: 0.0724

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16848861; hg19: chr1-237144914;