6-136974197-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000414680.1(RPL35AP3):​n.21T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 119986 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 69610

African (AFR) AF: 0.00 AC: 0 AN: 2346

American (AMR) AF: 0.00 AC: 0 AN: 9018

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2098

East Asian (EAS) AF: 0.00 AC: 0 AN: 4580

South Asian (SAS) AF: 0.00 AC: 0 AN: 14870

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21188

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 336

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 60520

Other (OTH) AF: 0.00 AC: 0 AN: 5030

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.24
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;