ENST00000404529.2:n.204G>C

Variant names:

• chrX-57069482-C-G
• rs204165
• ENST00000404529.2:n.204G>C

Variant summary

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

The ENST00000404529.2(SPIN2P1):​n.204G>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: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: SPIN2P1 ENST00000404529.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 3 publications found

Genes affected

SPIN2P1 (HGNC:54967): (SPIN2 family pseudogene 1)

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=-0.54).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPIN2P1		n.57069482C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPIN2P1	ENST00000404529.2	n.204G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 108696 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 34896

African (AFR) AF: 0.00 AC: 0 AN: 2305

American (AMR) AF: 0.00 AC: 0 AN: 9865

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1873

East Asian (EAS) AF: 0.00 AC: 0 AN: 3795

South Asian (SAS) AF: 0.00 AC: 0 AN: 11016

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 15523

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1458

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 57819

Other (OTH) AF: 0.00 AC: 0 AN: 5042

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.38
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs204165; hg19: chrX-57095915;