X-141258998-A-G

Variant names:

• chrX-141258998-A-G
• rs845150
• ENST00000662492.1:n.102+71161A>G

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.102+71161A>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 0.90 (31456 hom., 29323 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 0 publications found

Genes affected

SPANXA2-OT1 (HGNC:31683): (SPANXA2 overlapping transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662492.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPANXA2-OT1	ENST00000662492.1		n.102+71161A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.897 AC: 98998 AN: 110353 Hom.: 31465 Cov.: 23

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.994

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.912

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: 0.897 AC: 99037 AN: 110403 Hom.: 31456 Cov.: 23 AF XY: 0.899 AC XY: 29323 AN XY: 32631

African (AFR) AF: 0.784 AC: 23807 AN: 30380

American (AMR) AF: 0.940 AC: 9703 AN: 10326

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 2517 AN: 2637

East Asian (EAS) AF: 0.997 AC: 3443 AN: 3452

South Asian (SAS) AF: 0.969 AC: 2467 AN: 2546

European-Finnish (FIN) AF: 0.905 AC: 5260 AN: 5809

Middle Eastern (MID) AF: 0.944 AC: 202 AN: 214

European-Non Finnish (NFE) AF: 0.938 AC: 49587 AN: 52848

Other (OTH) AF: 0.910 AC: 1375 AN: 1511

Alfa AF: 0.923 Hom.: 40322

Bravo AF: 0.897

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs845150;

hg19: chrX-140353129;