11-121431110-C-A

Variant names:

• chr11-121431110-C-A
• rs17125331
• ENST00000816477.1:n.251-17599G>T

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.251-17599G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,146 control chromosomes in the GnomAD database, including 7,949 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (7949 hom., cov: 32)
• Consequence: SORL1-AS1 ENST00000816477.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.99
• Publications: 6 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=-0.98).
• BP6: Variant 11-121431110-C-A is Benign according to our data. Variant chr11-121431110-C-A is described in ClinVar as Benign. ClinVar VariationId is 873290.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 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.251-17599G>T		intron	N/A
	SORL1-AS1	ENST00000816478.1		n.146+4202G>T		intron	N/A
	SORL1-AS1	ENST00000816479.1		n.121-2677G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43409 AN: 152028 Hom.: 7916 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.286 AC: 43500 AN: 152146 Hom.: 7949 Cov.: 32 AF XY: 0.279 AC XY: 20761 AN XY: 74364

African (AFR) AF: 0.528 AC: 21879 AN: 41476

American (AMR) AF: 0.247 AC: 3769 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5170

South Asian (SAS) AF: 0.149 AC: 722 AN: 4832

European-Finnish (FIN) AF: 0.149 AC: 1583 AN: 10594

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13098 AN: 68006

Other (OTH) AF: 0.269 AC: 568 AN: 2114

Alfa AF: 0.222 Hom.: 17524

Bravo AF: 0.310

Asia WGS AF: 0.193 AC: 673 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	-0.98
CADD	Benign	0.035
DANN	Benign	0.47
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs17125331; hg19: chr11-121301819;