19-23832042-C-T

Variant names:

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

Variant summary

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

The ENST00000471224.5(RPSA2):​n.847C>T 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 0.991 in 454,182 control chromosomes in the GnomAD database, including 223,076 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 0.98 (72924 hom., cov: 32)
  • Exomes 𝑓: 1.0 (150152 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSA2	NR_149350.3	n.787C>T		non_coding_transcript_exon_variant	Exon 4 of 4
RPSA2	NR_149351.3	n.915C>T		non_coding_transcript_exon_variant	Exon 5 of 5
RPSA2	NR_149352.3	n.577C>T		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>T		non_coding_transcript_exon_variant	Exon 4 of 4	3
ENSG00000233836	ENST00000472297.2	n.659C>T		non_coding_transcript_exon_variant	Exon 4 of 4	6
RPSA2	ENST00000475499.2	n.726C>T		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.978 AC: 148824 AN: 152120 Hom.: 72887 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.986

GnomAD4 exome AF: 0.997 AC: 301083 AN: 301944 Hom.: 150152 Cov.: 0 AF XY: 0.998 AC XY: 172369 AN XY: 172768

African (AFR) AF: 0.917 AC: 6984 AN: 7618

American (AMR) AF: 0.995 AC: 21575 AN: 21682

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 7518 AN: 7518

East Asian (EAS) AF: 1.00 AC: 12341 AN: 12342

South Asian (SAS) AF: 1.00 AC: 50962 AN: 50970

European-Finnish (FIN) AF: 1.00 AC: 27573 AN: 27576

Middle Eastern (MID) AF: 0.996 AC: 2530 AN: 2540

European-Non Finnish (NFE) AF: 1.00 AC: 158371 AN: 158414

Other (OTH) AF: 0.996 AC: 13229 AN: 13284

GnomAD4 genome AF: 0.978 AC: 148917 AN: 152238 Hom.: 72924 Cov.: 32 AF XY: 0.979 AC XY: 72884 AN XY: 74434

African (AFR) AF: 0.924 AC: 38368 AN: 41528

American (AMR) AF: 0.993 AC: 15183 AN: 15294

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5186

South Asian (SAS) AF: 1.00 AC: 4828 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10606 AN: 10606

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67983 AN: 68002

Other (OTH) AF: 0.986 AC: 2087 AN: 2116

Alfa AF: 0.984 Hom.: 8963

Bravo AF: 0.975

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	3.1
DANN	Benign	0.27
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;