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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414680.1. 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
	RPL35AP3	ENST00000414680.1	TSL:6	n.21T>C		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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;