rs668053

Variant names:

• chr11-121437816-G-A
• rs668053
• ENST00000816477.1:n.250+11880C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-121437816-G-A
• chr11-121437816-G-C
• chr11-121437816-G-T

Variant summary

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

The ENST00000816477.1(SORL1-AS1):​n.250+11880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,056 control chromosomes in the GnomAD database, including 14,647 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 0.41 (14647 hom., cov: 32)
• Consequence: SORL1-AS1 ENST00000816477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 6 publications found

Genes affected

SORL1-AS1 (HGNC:55594): (SORL1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816477.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SORL1-AS1	ENST00000816477.1		n.250+11880C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62714 AN: 151938 Hom.: 14644 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.413 AC: 62724 AN: 152056 Hom.: 14647 Cov.: 32 AF XY: 0.421 AC XY: 31296 AN XY: 74328

African (AFR) AF: 0.190 AC: 7904 AN: 41514

American (AMR) AF: 0.522 AC: 7974 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3356 AN: 5160

South Asian (SAS) AF: 0.605 AC: 2908 AN: 4810

European-Finnish (FIN) AF: 0.508 AC: 5363 AN: 10554

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31956 AN: 67956

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.456 Hom.: 73842

Bravo AF: 0.398

Asia WGS AF: 0.625 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.54
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs668053;

hg19: chr11-121308525;