Menu
GeneBe

rs617847

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003105.6(SORL1):c.1597-530G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,982 control chromosomes in the GnomAD database, including 12,081 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 0.39 ( 12081 hom., cov: 32)

Consequence

SORL1
NM_003105.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0780
Variant links:
Genes affected
SORL1 (HGNC:11185): (sortilin related receptor 1) This gene encodes a mosaic protein that belongs to at least two families: the vacuolar protein sorting 10 (VPS10) domain-containing receptor family, and the low density lipoprotein receptor (LDLR) family. The encoded protein also contains fibronectin type III repeats and an epidermal growth factor repeat. The encoded preproprotein is proteolytically processed to generate the mature receptor, which likely plays roles in endocytosis and sorting. Mutations in this gene may be associated with Alzheimer's disease. [provided by RefSeq, Feb 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SORL1NM_003105.6 linkuse as main transcriptc.1597-530G>A intron_variant ENST00000260197.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SORL1ENST00000260197.12 linkuse as main transcriptc.1597-530G>A intron_variant 1 NM_003105.6 P1
SORL1ENST00000532451.1 linkuse as main transcriptn.1549-530G>A intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.387
AC:
58778
AN:
151864
Hom.:
12052
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.255
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.423
Gnomad ASJ
AF:
0.344
Gnomad EAS
AF:
0.563
Gnomad SAS
AF:
0.440
Gnomad FIN
AF:
0.417
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.441
Gnomad OTH
AF:
0.400
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.387
AC:
58840
AN:
151982
Hom.:
12081
Cov.:
32
AF XY:
0.386
AC XY:
28671
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.256
Gnomad4 AMR
AF:
0.424
Gnomad4 ASJ
AF:
0.344
Gnomad4 EAS
AF:
0.562
Gnomad4 SAS
AF:
0.441
Gnomad4 FIN
AF:
0.417
Gnomad4 NFE
AF:
0.441
Gnomad4 OTH
AF:
0.407
Alfa
AF:
0.400
Hom.:
2059
Bravo
AF:
0.384
Asia WGS
AF:
0.499
AC:
1737
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
0.45
Dann
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs617847; hg19: chr11-121402643; API