rs7933723

chr11-123017862-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027288.1(SAE1P1):n.297G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,481,918 control chromosomes in the GnomAD database, including 99,017 homozygotes. 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 0.28 (7398 hom., cov: 32)
  • Exomes 𝑓: 0.36 (91619 hom.)
• Consequence: SAE1P1 NR_027288.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.38

Genes affected

SAE1P1 (HGNC:56699): (SAE1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAE1P1	NR_027288.1	n.297G>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAE1P1	ENST00000532044.1	n.225G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42601 AN: 152012 Hom.: 7397 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.327

GnomAD4 exome AF: 0.357 AC: 474967 AN: 1329788 Hom.: 91619 Cov.: 26 AF XY: 0.356 AC XY: 237768 AN XY: 668314

Gnomad4 AFR exome AF: 0.0933

Gnomad4 AMR exome AF: 0.197

Gnomad4 ASJ exome AF: 0.395

Gnomad4 EAS exome AF: 0.000870

Gnomad4 SAS exome AF: 0.239

Gnomad4 FIN exome AF: 0.352

Gnomad4 NFE exome AF: 0.397

Gnomad4 OTH exome AF: 0.334

GnomAD4 genome AF: 0.280 AC: 42608 AN: 152130 Hom.: 7398 Cov.: 32 AF XY: 0.272 AC XY: 20269 AN XY: 74390

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.328

Alfa AF: 0.377 Hom.: 19065

Bravo AF: 0.268

Asia WGS AF: 0.125 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	15
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7933723; hg19: chr11-122888570;