rs11047432

Variant names:

• chr12-8822219-T-C
• rs11047432
• ENST00000537288.1:n.286+8443A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-8822219-T-C
• chr12-8822219-T-A

Variant summary

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

The ENST00000537288.1(A2ML1-AS1):​n.286+8443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,006 control chromosomes in the GnomAD database, including 8,488 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (8488 hom., cov: 32)
• Consequence: A2ML1-AS1 ENST00000537288.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.712
• Publications: 3 publications found

Genes affected

A2ML1-AS1 (HGNC:41022): (A2ML1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 12-8822219-T-C is Benign according to our data. Variant chr12-8822219-T-C is described in ClinVar as Benign. ClinVar VariationId is 561801.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537288.1. 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
	A2ML1-AS1	NR_046715.1		n.645+8443A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	A2ML1-AS1	ENST00000537288.1	TSL:3	n.286+8443A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49303 AN: 151888 Hom.: 8479 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.325 AC: 49339 AN: 152006 Hom.: 8488 Cov.: 32 AF XY: 0.330 AC XY: 24504 AN XY: 74306

African (AFR) AF: 0.386 AC: 16007 AN: 41432

American (AMR) AF: 0.286 AC: 4366 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3464

East Asian (EAS) AF: 0.467 AC: 2415 AN: 5170

South Asian (SAS) AF: 0.492 AC: 2371 AN: 4818

European-Finnish (FIN) AF: 0.368 AC: 3885 AN: 10564

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.275 AC: 18657 AN: 67964

Other (OTH) AF: 0.265 AC: 560 AN: 2110

Alfa AF: 0.284 Hom.: 8485

Bravo AF: 0.319

Asia WGS AF: 0.430 AC: 1493 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		0.71
PromoterAI		-0.028	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11047432; hg19: chr12-8974815; COSMIC: COSV55299211;