11-123017862-G-T

Variant names:

• chr11-123017862-G-T
• rs7933723
• ENST00000532044.1:n.225G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_027288.1. 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
	SAE1P1	NR_027288.1		n.297G>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAE1P1	ENST00000532044.1	TSL:6	n.225G>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0933 AC: 2872 AN: 30784

American (AMR) AF: 0.197 AC: 8769 AN: 44580

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 10027 AN: 25370

East Asian (EAS) AF: 0.000870 AC: 34 AN: 39074

South Asian (SAS) AF: 0.239 AC: 19947 AN: 83534

European-Finnish (FIN) AF: 0.352 AC: 18759 AN: 53348

Middle Eastern (MID) AF: 0.379 AC: 1880 AN: 4958

European-Non Finnish (NFE) AF: 0.397 AC: 394011 AN: 992276

Other (OTH) AF: 0.334 AC: 18668 AN: 55864

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

African (AFR) AF: 0.110 AC: 4572 AN: 41536

American (AMR) AF: 0.252 AC: 3852 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1386 AN: 3470

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5176

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4816

European-Finnish (FIN) AF: 0.344 AC: 3640 AN: 10572

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26878 AN: 67958

Other (OTH) AF: 0.328 AC: 692 AN: 2110

Alfa AF: 0.354 Hom.: 28387

Bravo AF: 0.268

Asia WGS AF: 0.125 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Benign	0.70
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs7933723; hg19: chr11-122888570;