rs11830829

Variant names:

• chr12-32946195-A-G
• rs11830829
• ENST00000841386.1:n.305+10591A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-32946195-A-G
• chr12-32946195-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000841386.1(ENSG00000309487):​n.305+10591A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,934 control chromosomes in the GnomAD database, including 15,734 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (15734 hom., cov: 32)
• Consequence: ENSG00000309487 ENST00000841386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 4 publications found

Genes affected

ENSG00000309487 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841386.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309487	ENST00000841386.1		n.305+10591A>G		intron	N/A
	ENSG00000309487	ENST00000841387.1		n.291+10591A>G		intron	N/A
	ENSG00000309487	ENST00000841388.1		n.256+13308A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65519 AN: 151816 Hom.: 15701 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.432 AC: 65616 AN: 151934 Hom.: 15734 Cov.: 32 AF XY: 0.433 AC XY: 32147 AN XY: 74238

African (AFR) AF: 0.619 AC: 25653 AN: 41428

American (AMR) AF: 0.384 AC: 5858 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3703 AN: 5170

South Asian (SAS) AF: 0.424 AC: 2042 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3622 AN: 10540

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22501 AN: 67940

Other (OTH) AF: 0.419 AC: 884 AN: 2108

Alfa AF: 0.357 Hom.: 43466

Bravo AF: 0.445

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs11830829; hg19: chr12-33099129; COSMIC: COSV70886407;