rs10495669

Variant names:

• chr2-17844006-C-G
• rs10495669

Variant summary

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

The variant allele was found at a frequency of 0.505 in 152,138 control chromosomes in the GnomAD database, including 20,270 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 0.50 (20270 hom., cov: 33)
• Consequence: ZPAXP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 1 publications found

Genes affected

ZPAXP (HGNC:51635): (zona pellucida glycoprotein AX, pseudogene)

ENSG00000297720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZPAXP		n.17844006C>G		intragenic_variant
LOC112267888	XR_939764.2	n.447+3688G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297720	ENST00000750479.1	n.453+3688G>C		intron_variant	Intron 3 of 3
ENSG00000297720	ENST00000750480.1	n.415+3688G>C		intron_variant	Intron 3 of 4
ENSG00000297720	ENST00000750481.1	n.595+1881G>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76762 AN: 152020 Hom.: 20256 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.533

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.505 AC: 76816 AN: 152138 Hom.: 20270 Cov.: 33 AF XY: 0.499 AC XY: 37106 AN XY: 74376

African (AFR) AF: 0.487 AC: 20178 AN: 41470

American (AMR) AF: 0.412 AC: 6308 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3470

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5172

South Asian (SAS) AF: 0.438 AC: 2114 AN: 4828

European-Finnish (FIN) AF: 0.533 AC: 5640 AN: 10586

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38156 AN: 67994

Other (OTH) AF: 0.528 AC: 1117 AN: 2116

Alfa AF: 0.530 Hom.: 2721

Bravo AF: 0.494

Asia WGS AF: 0.250 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.53
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10495669; hg19: chr2-18025273;