X-23781816-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_184056.1(SAT1-DT):n.419+752G>A 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 0.65 (16341 hom., 10129 hem., cov: 13)
  • Failed GnomAD Quality Control
• Consequence: SAT1-DT NR_184056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High Homozygotes in GnomAd at 16335 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAT1-DT	NR_184056.1	n.419+752G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAT1-DT	ENST00000366134.2	n.153+752G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.654 AC: 56867 AN: 87000 Hom.: 16335 Cov.: 13 AF XY: 0.639 AC XY: 10114 AN XY: 15828

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.661

Alfa AF: 0.469 Hom.: 1514

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.1
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928931; hg19: chrX-23799933;