ENST00000414680.1:n.21T>C

Variant names:

• chr6-136974197-A-G
• rs2040034
• ENST00000414680.1:n.21T>C

Variant summary

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

The ENST00000414680.1(RPL35AP3):​n.21T>C 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 0.801 in 271,808 control chromosomes in the GnomAD database, including 87,773 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 0.76 (44668 hom., cov: 33)
  • Exomes 𝑓: 0.85 (43105 hom.)
• Consequence: RPL35AP3 ENST00000414680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869
• Publications: 4 publications found

Genes affected

RPL35AP3 (HGNC:21117): (ribosomal protein L35a pseudogene 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL35AP3		n.136974197A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL35AP3	ENST00000414680.1	n.21T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116168 AN: 151882 Hom.: 44637 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.759

GnomAD4 exome AF: 0.847 AC: 101434 AN: 119808 Hom.: 43105 Cov.: 0 AF XY: 0.847 AC XY: 58834 AN XY: 69498

African (AFR) AF: 0.874 AC: 2044 AN: 2338

American (AMR) AF: 0.880 AC: 7930 AN: 9010

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 1834 AN: 2096

East Asian (EAS) AF: 0.869 AC: 3976 AN: 4574

South Asian (SAS) AF: 0.865 AC: 12827 AN: 14834

European-Finnish (FIN) AF: 0.782 AC: 16553 AN: 21168

Middle Eastern (MID) AF: 0.911 AC: 306 AN: 336

European-Non Finnish (NFE) AF: 0.854 AC: 51599 AN: 60424

Other (OTH) AF: 0.868 AC: 4365 AN: 5028

GnomAD4 genome AF: 0.765 AC: 116246 AN: 152000 Hom.: 44668 Cov.: 33 AF XY: 0.768 AC XY: 57043 AN XY: 74272

African (AFR) AF: 0.824 AC: 34183 AN: 41504

American (AMR) AF: 0.803 AC: 12231 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3468

East Asian (EAS) AF: 0.824 AC: 4256 AN: 5168

South Asian (SAS) AF: 0.733 AC: 3535 AN: 4824

European-Finnish (FIN) AF: 0.765 AC: 8078 AN: 10556

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.719 AC: 48865 AN: 67932

Other (OTH) AF: 0.760 AC: 1602 AN: 2108

Alfa AF: 0.752 Hom.: 10152

Bravo AF: 0.770

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.82
DANN	Benign	0.16
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs2040034; hg19: chr6-137295334;