rs1960264

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-23781758-C-G
• chrX-23781758-C-T

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>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: not found (cov: 18)
• 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=-0.89).

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>C		intron	N/A
	SAT1-DT	NR_184057.1		n.102+1127G>C		intron	N/A
	SAT1-DT	NR_184058.1		n.419+810G>C		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>C		intron	N/A
	SAT1-DT	ENST00000737050.1		n.839+810G>C		intron	N/A
	SAT1-DT	ENST00000737051.1		n.190+1127G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 18

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 18

Alfa AF: 0.00 Hom.: 5456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.45
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;