ENST00000366134.3:n.231+947T>G

Variant names:

• chrX-23781621-A-C
• rs6526342
• ENST00000366134.3:n.231+947T>G

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+947T>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 0.67 (18175 hom., 20758 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: SAT1-DT ENST00000366134.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 12 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=-0.68).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAT1-DT	NR_184056.1		n.419+947T>G		intron	N/A
	SAT1-DT	NR_184057.1		n.102+1264T>G		intron	N/A
	SAT1-DT	NR_184058.1		n.419+947T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAT1-DT	ENST00000366134.3	TSL:3	n.231+947T>G		intron	N/A
	SAT1-DT	ENST00000737050.1		n.839+947T>G		intron	N/A
	SAT1-DT	ENST00000737051.1		n.190+1264T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.671 AC: 72696 AN: 108348 Hom.: 18172 Cov.: 21

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.625

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.664

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: 0.671 AC: 72731 AN: 108397 Hom.: 18175 Cov.: 21 AF XY: 0.674 AC XY: 20758 AN XY: 30813

African (AFR) AF: 0.469 AC: 13961 AN: 29791

American (AMR) AF: 0.571 AC: 5659 AN: 9910

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 1957 AN: 2615

East Asian (EAS) AF: 0.610 AC: 2077 AN: 3407

South Asian (SAS) AF: 0.826 AC: 2111 AN: 2556

European-Finnish (FIN) AF: 0.770 AC: 4070 AN: 5285

Middle Eastern (MID) AF: 0.635 AC: 134 AN: 211

European-Non Finnish (NFE) AF: 0.786 AC: 41242 AN: 52488

Other (OTH) AF: 0.669 AC: 979 AN: 1463

Alfa AF: 0.701 Hom.: 19368

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6526342; hg19: chrX-23799738;