rs12827476

Variant names:

• chr12-4196717-T-C
• rs12827476
• ENST00000725226.1:n.309+7020A>G

Variant summary

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

The ENST00000725226.1(ENSG00000294684):​n.309+7020A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,054 control chromosomes in the GnomAD database, including 16,201 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 0.44 (16201 hom., cov: 31)
• Consequence: ENSG00000294684 ENST00000725226.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 6 publications found

Genes affected

ENSG00000294684 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725226.1. 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
	ENSG00000294684	ENST00000725226.1		n.309+7020A>G		intron	N/A
	ENSG00000294684	ENST00000725227.1		n.243+7020A>G		intron	N/A
	ENSG00000294684	ENST00000725228.1		n.322+6932A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66592 AN: 151936 Hom.: 16196 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.438 AC: 66614 AN: 152054 Hom.: 16201 Cov.: 31 AF XY: 0.434 AC XY: 32240 AN XY: 74318

African (AFR) AF: 0.233 AC: 9647 AN: 41470

American (AMR) AF: 0.514 AC: 7857 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3464

East Asian (EAS) AF: 0.217 AC: 1124 AN: 5172

South Asian (SAS) AF: 0.307 AC: 1484 AN: 4828

European-Finnish (FIN) AF: 0.501 AC: 5292 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38040 AN: 67948

Other (OTH) AF: 0.448 AC: 947 AN: 2114

Alfa AF: 0.494 Hom.: 29296

Bravo AF: 0.436

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.7
DANN	Benign	0.81
PhyloP100		1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12827476;

hg19: chr12-4305883;