chr12-131279829-G-A

Variant names:

• chr12-131279829-G-A
• rs12578896
• ENST00000794856.1:n.216+2157G>A

Variant summary

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

The ENST00000794856.1(ENSG00000303473):​n.216+2157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,888 control chromosomes in the GnomAD database, including 11,845 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 0.38 (11845 hom., cov: 33)
• Consequence: ENSG00000303473 ENST00000794856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 4 publications found

Genes affected

ENSG00000303473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794856.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303473	ENST00000794856.1		n.216+2157G>A		intron	N/A
	ENSG00000303473	ENST00000794857.1		n.188+2157G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58117 AN: 151770 Hom.: 11845 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.383 AC: 58128 AN: 151888 Hom.: 11845 Cov.: 33 AF XY: 0.382 AC XY: 28379 AN XY: 74220

African (AFR) AF: 0.264 AC: 10950 AN: 41444

American (AMR) AF: 0.370 AC: 5641 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3466

East Asian (EAS) AF: 0.585 AC: 3021 AN: 5160

South Asian (SAS) AF: 0.401 AC: 1934 AN: 4820

European-Finnish (FIN) AF: 0.398 AC: 4189 AN: 10532

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29424 AN: 67890

Other (OTH) AF: 0.385 AC: 812 AN: 2110

Alfa AF: 0.410 Hom.: 29306

Bravo AF: 0.374

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		0.053

Splicing

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

Other links and lift over

dbSNP: rs12578896; hg19: chr12-131764374;