11-123019731-T-C

Variant names:

• chr11-123019731-T-C
• rs11218921
• NR_027288.1:n.*120T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027288.1(SAE1P1):​n.*120T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,988 control chromosomes in the GnomAD database, including 32,353 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 0.64 (32353 hom., cov: 31)
• Consequence: SAE1P1 NR_027288.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 3 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAE1P1	NR_027288.1	n.*120T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96690 AN: 151872 Hom.: 32348 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.679

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.637 AC: 96743 AN: 151988 Hom.: 32353 Cov.: 31 AF XY: 0.634 AC XY: 47119 AN XY: 74278

African (AFR) AF: 0.445 AC: 18443 AN: 41434

American (AMR) AF: 0.635 AC: 9701 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2503 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1847 AN: 5150

South Asian (SAS) AF: 0.607 AC: 2917 AN: 4808

European-Finnish (FIN) AF: 0.766 AC: 8081 AN: 10544

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50918 AN: 67986

Other (OTH) AF: 0.676 AC: 1430 AN: 2114

Alfa AF: 0.711 Hom.: 109302

Bravo AF: 0.617

Asia WGS AF: 0.519 AC: 1807 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.93
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs11218921; hg19: chr11-122890439;