rs928931

Variant names:

• chrX-23781816-C-A
• rs928931
• ENST00000366134.3:n.231+752G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-23781816-C-A
• chrX-23781816-C-G
• chrX-23781816-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+752G>T 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 0.0 (0 hom., 0 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=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAT1-DT	NR_184056.1	n.419+752G>T		intron_variant	Intron 1 of 4
SAT1-DT	NR_184057.1	n.102+1069G>T		intron_variant	Intron 1 of 4
SAT1-DT	NR_184058.1	n.419+752G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAT1-DT	ENST00000366134.3	n.231+752G>T		intron_variant	Intron 2 of 2	3
SAT1-DT	ENST00000737050.1	n.839+752G>T		intron_variant	Intron 1 of 1
SAT1-DT	ENST00000737051.1	n.190+1069G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 87131 Hom.: 0 Cov.: 13

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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: AC0 AF: 0.00 AC: 0 AN: 87131 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 15847

African (AFR) AF: 0.00 AC: 0 AN: 22494

American (AMR) AF: 0.00 AC: 0 AN: 6879

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2385

East Asian (EAS) AF: 0.00 AC: 0 AN: 2709

South Asian (SAS) AF: 0.00 AC: 0 AN: 1570

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2677

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 171

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 46594

Other (OTH) AF: 0.00 AC: 0 AN: 1079

Alfa AF: 0.00 Hom.: 1514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.93
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs928931; hg19: chrX-23799933;