X-85075487-T-G

Variant names:

• chrX-85075487-T-G
• rs2032571
• NM_198450.6:c.718+1096T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_198450.6(APOOL):​c.718+1096T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.64 (15912 hom., 20784 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: APOOL NM_198450.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.640
• Publications: 0 publications found

Genes affected

APOOL (HGNC:24009): (apolipoprotein O like) This gene encodes a protein which contains an apolipoprotein O superfamily domain. This domain is found on proteins in circulating lipoprotein complexes. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOOL	NM_198450.6	c.718+1096T>G		intron_variant	Intron 8 of 8	ENST00000373173.7	NP_940852.3
APOOL	XM_017029272.2	c.727+1087T>G		intron_variant	Intron 8 of 8		XP_016884761.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOOL	ENST00000373173.7	c.718+1096T>G		intron_variant	Intron 8 of 8	1	NM_198450.6	ENSP00000362268.2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 70078 AN: 109883 Hom.: 15921 Cov.: 22

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.668

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.638 AC: 70090 AN: 109933 Hom.: 15912 Cov.: 22 AF XY: 0.644 AC XY: 20784 AN XY: 32249

African (AFR) AF: 0.513 AC: 15546 AN: 30332

American (AMR) AF: 0.688 AC: 7031 AN: 10214

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 1945 AN: 2626

East Asian (EAS) AF: 0.641 AC: 2225 AN: 3473

South Asian (SAS) AF: 0.814 AC: 2072 AN: 2546

European-Finnish (FIN) AF: 0.731 AC: 4227 AN: 5782

Middle Eastern (MID) AF: 0.800 AC: 172 AN: 215

European-Non Finnish (NFE) AF: 0.675 AC: 35481 AN: 52574

Other (OTH) AF: 0.665 AC: 999 AN: 1503

Alfa AF: 0.627 Hom.: 12414

Bravo AF: 0.628

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.77
PhyloP100		0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2032571; hg19: chrX-84330493;