12-58551492-G-A

Variant names:

• chr12-58551492-G-A
• rs3913061
• ENST00000546977.5:n.56+7313G>A

Variant summary

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

The ENST00000546977.5(ENSG00000258231):​n.56+7313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,106 control chromosomes in the GnomAD database, including 33,409 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 0.66 (33409 hom., cov: 33)
• Consequence: ENSG00000258231 ENST00000546977.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 1 publications found

Genes affected

ENSG00000258231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546977.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258231	ENST00000546977.5	TSL:5	n.56+7313G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100639 AN: 151988 Hom.: 33391 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.662 AC: 100712 AN: 152106 Hom.: 33409 Cov.: 33 AF XY: 0.661 AC XY: 49115 AN XY: 74338

African (AFR) AF: 0.614 AC: 25484 AN: 41488

American (AMR) AF: 0.697 AC: 10656 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2308 AN: 3466

East Asian (EAS) AF: 0.646 AC: 3334 AN: 5164

South Asian (SAS) AF: 0.659 AC: 3177 AN: 4820

European-Finnish (FIN) AF: 0.688 AC: 7262 AN: 10562

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46188 AN: 68006

Other (OTH) AF: 0.670 AC: 1416 AN: 2112

Alfa AF: 0.672 Hom.: 4427

Bravo AF: 0.662

Asia WGS AF: 0.662 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.20
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3913061; hg19: chr12-58945275;