rs6526342

Positions:

• chrX-23781621-A-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_184056.1(SAT1-DT):​n.419+947T>G variant causes a intron, non coding transcript 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 NR_184056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAT1-DT	NR_184056.1	n.419+947T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAT1-DT	ENST00000366134.2	n.153+947T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.671 AC: 72696 AN: 108348 Hom.: 18172 Cov.: 21 AF XY: 0.674 AC XY: 20725 AN XY: 30754

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

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.669

Alfa AF: 0.730 Hom.: 12835

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6526342; hg19: chrX-23799738;