X-23781816-C-T

Variant names:

• chrX-23781816-C-T
• rs928931
• ENST00000366134.3:n.231+752G>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+752G>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 0.65 (16341 hom., 10129 hem., cov: 13)
  • Failed GnomAD Quality Control
• Consequence: SAT1-DT ENST00000366134.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 5 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=-0.81).

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+752G>A		intron	N/A
	SAT1-DT	NR_184057.1		n.102+1069G>A		intron	N/A
	SAT1-DT	NR_184058.1		n.419+752G>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+752G>A		intron	N/A
	SAT1-DT	ENST00000737050.1		n.839+752G>A		intron	N/A
	SAT1-DT	ENST00000737051.1		n.190+1069G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.654 AC: 56867 AN: 87000 Hom.: 16335 Cov.: 13

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.654

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: 0.654 AC: 56888 AN: 87016 Hom.: 16341 Cov.: 13 AF XY: 0.639 AC XY: 10129 AN XY: 15852

African (AFR) AF: 0.369 AC: 8293 AN: 22481

American (AMR) AF: 0.587 AC: 4028 AN: 6862

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 1756 AN: 2385

East Asian (EAS) AF: 0.613 AC: 1649 AN: 2691

South Asian (SAS) AF: 0.830 AC: 1291 AN: 1555

European-Finnish (FIN) AF: 0.775 AC: 2071 AN: 2673

Middle Eastern (MID) AF: 0.675 AC: 104 AN: 154

European-Non Finnish (NFE) AF: 0.784 AC: 36517 AN: 46550

Other (OTH) AF: 0.661 AC: 722 AN: 1093

Alfa AF: 0.469 Hom.: 1514

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.94
PhyloP100		-0.93

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: rs928931;

hg19: chrX-23799933;