6-27211416-G-C

Variant names:

• chr6-27211416-G-C
• rs858988
• ENST00000310599.3:n.173G>C

Variant summary

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

The ENST00000310599.3(RPL10P2):​n.173G>C 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RPL10P2 ENST00000310599.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.36
• Publications: 3 publications found

Genes affected

RPL10P2 (HGNC:13975): (ribosomal protein L10 pseudogene 2)

ENSG00000297504 (HGNC:):

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=-0.56).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000310599.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL10P2	ENST00000310599.3	TSL:6	n.173G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000297504	ENST00000748463.1		n.65-5881G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 510604 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 274490

African (AFR) AF: 0.00 AC: 0 AN: 14140

American (AMR) AF: 0.00 AC: 0 AN: 29142

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14230

East Asian (EAS) AF: 0.00 AC: 0 AN: 33370

South Asian (SAS) AF: 0.00 AC: 0 AN: 50156

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47174

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2054

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 293042

Other (OTH) AF: 0.00 AC: 0 AN: 27296

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 7536

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	4.7
DANN	Benign	0.56
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs858988; hg19: chr6-27179195;