11-121431937-A-G

Variant names:

• chr11-121431937-A-G
• rs17125333
• ENST00000816477.1:n.250+17759T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000816477.1(SORL1-AS1):​n.250+17759T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,120 control chromosomes in the GnomAD database, including 4,899 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4899 hom., cov: 32)
• Consequence: SORL1-AS1 ENST00000816477.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0840
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-121431937-A-G is Benign according to our data. Variant chr11-121431937-A-G is described in ClinVar as Benign. ClinVar VariationId is 873295.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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+17759T>C		intron	N/A
	SORL1-AS1	ENST00000816478.1		n.146+3375T>C		intron	N/A
	SORL1-AS1	ENST00000816479.1		n.120+3375T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36542 AN: 152002 Hom.: 4875 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.241 AC: 36616 AN: 152120 Hom.: 4899 Cov.: 32 AF XY: 0.237 AC XY: 17591 AN XY: 74360

African (AFR) AF: 0.361 AC: 14956 AN: 41474

American (AMR) AF: 0.229 AC: 3504 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1021 AN: 5182

South Asian (SAS) AF: 0.154 AC: 745 AN: 4832

European-Finnish (FIN) AF: 0.153 AC: 1624 AN: 10582

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13402 AN: 67974

Other (OTH) AF: 0.234 AC: 494 AN: 2110

Alfa AF: 0.204 Hom.: 2840

Bravo AF: 0.257

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.88
DANN	Benign	0.78
PhyloP100		-0.084

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: rs17125333;

hg19: chr11-121302646;