chrX-141256320-T-C

Variant names:

• chrX-141256320-T-C
• rs845144
• ENST00000662492.1:n.102+68483T>C

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+68483T>C 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 0.75 (22105 hom., 23930 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• 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 (Cadd=6.931).

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+68483T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 82436 AN: 109338 Hom.: 22118 Cov.: 22

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.776

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: 0.754 AC: 82464 AN: 109386 Hom.: 22105 Cov.: 22 AF XY: 0.754 AC XY: 23930 AN XY: 31748

African (AFR) AF: 0.678 AC: 20309 AN: 29957

American (AMR) AF: 0.739 AC: 7595 AN: 10277

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2027 AN: 2612

East Asian (EAS) AF: 0.862 AC: 2963 AN: 3437

South Asian (SAS) AF: 0.797 AC: 2016 AN: 2528

European-Finnish (FIN) AF: 0.736 AC: 4118 AN: 5596

Middle Eastern (MID) AF: 0.833 AC: 175 AN: 210

European-Non Finnish (NFE) AF: 0.793 AC: 41743 AN: 52615

Other (OTH) AF: 0.775 AC: 1155 AN: 1490

Alfa AF: 0.773 Hom.: 6403

Bravo AF: 0.749

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	6.9
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs845144;