rs858988

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-27211416-G-A
• chr6-27211416-G-C

Variant summary

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

The ENST00000310599.3(RPL10P2):​n.173G>A 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 0.906 in 662,290 control chromosomes in the GnomAD database, including 272,534 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 0.89 (61069 hom., cov: 31)
  • Exomes 𝑓: 0.91 (211465 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

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>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000297504	ENST00000748463.1		n.65-5881G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135984 AN: 152026 Hom.: 61034 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.922

GnomAD4 exome AF: 0.909 AC: 463776 AN: 510146 Hom.: 211465 Cov.: 0 AF XY: 0.913 AC XY: 250268 AN XY: 274248

African (AFR) AF: 0.861 AC: 12151 AN: 14114

American (AMR) AF: 0.952 AC: 27734 AN: 29124

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 13912 AN: 14226

East Asian (EAS) AF: 0.952 AC: 31745 AN: 33358

South Asian (SAS) AF: 0.977 AC: 48959 AN: 50130

European-Finnish (FIN) AF: 0.795 AC: 37489 AN: 47128

Middle Eastern (MID) AF: 0.959 AC: 1968 AN: 2052

European-Non Finnish (NFE) AF: 0.905 AC: 264913 AN: 292748

Other (OTH) AF: 0.913 AC: 24905 AN: 27266

GnomAD4 genome AF: 0.894 AC: 136075 AN: 152144 Hom.: 61069 Cov.: 31 AF XY: 0.891 AC XY: 66283 AN XY: 74350

African (AFR) AF: 0.863 AC: 35838 AN: 41510

American (AMR) AF: 0.940 AC: 14366 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3402 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4885 AN: 5154

South Asian (SAS) AF: 0.977 AC: 4712 AN: 4822

European-Finnish (FIN) AF: 0.776 AC: 8205 AN: 10578

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61609 AN: 68008

Other (OTH) AF: 0.923 AC: 1943 AN: 2106

Alfa AF: 0.902 Hom.: 7536

Bravo AF: 0.903

Asia WGS AF: 0.964 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	5.1
DANN	Benign	0.52
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;