11-121435753-G-A

Variant names:

• chr11-121435753-G-A
• rs4146874
• ENST00000816477.1:n.250+13943C>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.250+13943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,974 control chromosomes in the GnomAD database, including 4,555 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.23 (4555 hom., cov: 32)
• Consequence: SORL1-AS1 ENST00000816477.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.37
• Publications: 2 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=-0.89).
• BP6: Variant 11-121435753-G-A is Benign according to our data. Variant chr11-121435753-G-A is described in ClinVar as Benign. ClinVar VariationId is 873293.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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+13943C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35407 AN: 151856 Hom.: 4532 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.233 AC: 35477 AN: 151974 Hom.: 4555 Cov.: 32 AF XY: 0.229 AC XY: 17038 AN XY: 74260

African (AFR) AF: 0.340 AC: 14102 AN: 41440

American (AMR) AF: 0.225 AC: 3433 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 615 AN: 3464

East Asian (EAS) AF: 0.198 AC: 1020 AN: 5164

South Asian (SAS) AF: 0.144 AC: 695 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1624 AN: 10560

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.195 AC: 13246 AN: 67954

Other (OTH) AF: 0.231 AC: 487 AN: 2106

Alfa AF: 0.207 Hom.: 5001

Bravo AF: 0.249

ClinVar

ClinVar submissions as Germline

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	-0.89
CADD	Benign	0.19
DANN	Benign	0.71
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4146874; hg19: chr11-121306462;