5-134227627-A-G

Variant names:

• chr5-134227627-A-G
• rs2292283
• ENST00000703317.1:n.*73+15265T>C

Variant summary

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

The ENST00000703317.1(ENSG00000273345):​n.*73+15265T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,262 control chromosomes in the GnomAD database, including 58,467 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 0.87 (58466 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: ENSG00000273345 ENST00000703317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 7 publications found

Genes affected

ENSG00000273345 (HGNC:):

PPP2CA-DT (HGNC:55266): (PPP2CA divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2CA-DT	NR_186539.1	n.1218A>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273345	ENST00000703317.1	n.*73+15265T>C		intron_variant	Intron 4 of 9			ENSP00000515260.1

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132928 AN: 152138 Hom.: 58418 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.879

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.874 AC: 133031 AN: 152256 Hom.: 58466 Cov.: 32 AF XY: 0.869 AC XY: 64689 AN XY: 74424

African (AFR) AF: 0.912 AC: 37912 AN: 41560

American (AMR) AF: 0.803 AC: 12283 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2981 AN: 3472

East Asian (EAS) AF: 0.607 AC: 3147 AN: 5182

South Asian (SAS) AF: 0.841 AC: 4060 AN: 4828

European-Finnish (FIN) AF: 0.875 AC: 9264 AN: 10588

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60406 AN: 68012

Other (OTH) AF: 0.879 AC: 1859 AN: 2114

Alfa AF: 0.877 Hom.: 236222

Bravo AF: 0.867

Asia WGS AF: 0.779 AC: 2710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2292283; hg19: chr5-133563318;