X-23781758-C-T

Variant names:

• chrX-23781758-C-T
• rs1960264
• ENST00000366134.3:n.231+810G>A

Variant summary

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

The ENST00000366134.3(SAT1-DT):​n.231+810G>A 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 (16854 hom., 16716 hem., cov: 18)
  • Failed GnomAD Quality Control
• Consequence: SAT1-DT ENST00000366134.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 9 publications found

Genes affected

SAT1-DT (HGNC:56726): (SAT1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366134.3. 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
	SAT1-DT	NR_184056.1		n.419+810G>A		intron	N/A
	SAT1-DT	NR_184057.1		n.102+1127G>A		intron	N/A
	SAT1-DT	NR_184058.1		n.419+810G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAT1-DT	ENST00000366134.3	TSL:3	n.231+810G>A		intron	N/A
	SAT1-DT	ENST00000737050.1		n.839+810G>A		intron	N/A
	SAT1-DT	ENST00000737051.1		n.190+1127G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.638 AC: 65462 AN: 102593 Hom.: 16849 Cov.: 18

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.613

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.625

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: 65498 AN: 102635 Hom.: 16854 Cov.: 18 AF XY: 0.651 AC XY: 16716 AN XY: 25679

African (AFR) AF: 0.354 AC: 9901 AN: 27999

American (AMR) AF: 0.555 AC: 5020 AN: 9045

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 1915 AN: 2572

East Asian (EAS) AF: 0.598 AC: 1920 AN: 3210

South Asian (SAS) AF: 0.799 AC: 1758 AN: 2200

European-Finnish (FIN) AF: 0.775 AC: 3390 AN: 4373

Middle Eastern (MID) AF: 0.618 AC: 126 AN: 204

European-Non Finnish (NFE) AF: 0.786 AC: 40084 AN: 51016

Other (OTH) AF: 0.631 AC: 866 AN: 1372

Alfa AF: 0.701 Hom.: 5456

Bravo AF: 0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1960264; hg19: chrX-23799875;