X-57069482-C-T

Variant names:

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

Variant summary

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

The ENST00000404529.2(SPIN2P1):​n.204G>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 0.605 in 218,768 control chromosomes in the GnomAD database, including 31,717 homozygotes. There are 41,077 hemizygotes in GnomAD. 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 0.55 (14504 hom., 18558 hem., cov: 23)
  • Exomes 𝑓: 0.66 (17213 hom. 22519 hem.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.551 AC: 61079 AN: 110861 Hom.: 14512 Cov.: 23

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.504

GnomAD4 exome AF: 0.661 AC: 71336 AN: 107858 Hom.: 17213 Cov.: 0 AF XY: 0.647 AC XY: 22519 AN XY: 34832

African (AFR) AF: 0.112 AC: 258 AN: 2298

American (AMR) AF: 0.490 AC: 4809 AN: 9818

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 862 AN: 1855

East Asian (EAS) AF: 0.622 AC: 2352 AN: 3779

South Asian (SAS) AF: 0.542 AC: 5922 AN: 10932

European-Finnish (FIN) AF: 0.832 AC: 12853 AN: 15446

Middle Eastern (MID) AF: 0.356 AC: 517 AN: 1454

European-Non Finnish (NFE) AF: 0.709 AC: 40590 AN: 57272

Other (OTH) AF: 0.634 AC: 3173 AN: 5004

GnomAD4 genome AF: 0.550 AC: 61056 AN: 110910 Hom.: 14504 Cov.: 23 AF XY: 0.560 AC XY: 18558 AN XY: 33166

African (AFR) AF: 0.135 AC: 4145 AN: 30704

American (AMR) AF: 0.552 AC: 5796 AN: 10500

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1407 AN: 2626

East Asian (EAS) AF: 0.658 AC: 2273 AN: 3457

South Asian (SAS) AF: 0.619 AC: 1592 AN: 2571

European-Finnish (FIN) AF: 0.849 AC: 4982 AN: 5870

Middle Eastern (MID) AF: 0.380 AC: 82 AN: 216

European-Non Finnish (NFE) AF: 0.747 AC: 39430 AN: 52786

Other (OTH) AF: 0.497 AC: 746 AN: 1500

Alfa AF: 0.637 Hom.: 6294

Bravo AF: 0.508

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	13
DANN	Benign	0.42
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;