chr11-121431925-T-A

Variant names:

• chr11-121431925-T-A
• rs55736743
• ENST00000816477.1:n.250+17771A>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+17771A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,156 control chromosomes in the GnomAD database, including 4,890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4890 hom., cov: 32)
• Consequence: SORL1-AS1 ENST00000816477.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.619
• Publications: 1 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=-0.9).
• BP6: Variant 11-121431925-T-A is Benign according to our data. Variant chr11-121431925-T-A is described in ClinVar as Benign. ClinVar VariationId is 873294.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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+17771A>T		intron	N/A
	SORL1-AS1	ENST00000816478.1		n.146+3387A>T		intron	N/A
	SORL1-AS1	ENST00000816479.1		n.120+3387A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36515 AN: 152038 Hom.: 4866 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: 0.196

Gnomad SAS AF: 0.154

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: 0.240 AC: 36589 AN: 152156 Hom.: 4890 Cov.: 32 AF XY: 0.236 AC XY: 17575 AN XY: 74402

African (AFR) AF: 0.360 AC: 14940 AN: 41470

American (AMR) AF: 0.229 AC: 3501 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 616 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1015 AN: 5186

South Asian (SAS) AF: 0.154 AC: 743 AN: 4832

European-Finnish (FIN) AF: 0.153 AC: 1626 AN: 10604

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

European-Non Finnish (NFE) AF: 0.197 AC: 13399 AN: 67994

Other (OTH) AF: 0.235 AC: 494 AN: 2104

Alfa AF: 0.227 Hom.: 517

Bravo AF: 0.257

Asia WGS AF: 0.182 AC: 631 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	-0.90
CADD	Benign	0.096
DANN	Benign	0.62
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs55736743; hg19: chr11-121302634;