rs6511602

Variant names:

• chr19-23832042-C-G
• rs6511602
• ENST00000471224.5:n.847C>G

Your query was ambiguous. Multiple possible variants found:

• chr19-23832042-C-G
• chr19-23832042-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000471224.5(RPSA2):​n.847C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000033 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RPSA2 ENST00000471224.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 2 publications found

Genes affected

RPSA2 (HGNC:36809): (ribosomal protein SA 2)

ENSG00000233836 (HGNC:):

ZNF726P1 (HGNC:13136):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSA2	NR_149350.3	n.787C>G		non_coding_transcript_exon_variant	Exon 4 of 4
RPSA2	NR_149351.3	n.915C>G		non_coding_transcript_exon_variant	Exon 5 of 5
RPSA2	NR_149352.3	n.577C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPSA2	ENST00000471224.5	n.847C>G		non_coding_transcript_exon_variant	Exon 4 of 4	3
ENSG00000233836	ENST00000472297.2	n.659C>G		non_coding_transcript_exon_variant	Exon 4 of 4	6
RPSA2	ENST00000475499.2	n.726C>G		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 152130 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000331 AC: 1 AN: 301932 Hom.: 0 Cov.: 0 AF XY: 0.00000579 AC XY: 1 AN XY: 172758

African (AFR) AF: 0.00 AC: 0 AN: 7622

American (AMR) AF: 0.00 AC: 0 AN: 21682

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7518

East Asian (EAS) AF: 0.0000810 AC: 1 AN: 12342

South Asian (SAS) AF: 0.00 AC: 0 AN: 50968

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27570

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2540

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 158408

Other (OTH) AF: 0.00 AC: 0 AN: 13282

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 152130 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74308

African (AFR) AF: 0.00 AC: 0 AN: 41416

American (AMR) AF: 0.00 AC: 0 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5198

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68010

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.00 Hom.: 8963

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.7
DANN	Benign	0.36
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6511602; hg19: chr19-24014844;