rs12885270

Variant names:

• chr14-86706486-C-G
• rs12885270
• ENST00000778903.1:n.348+5758G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000778903.1(ENSG00000301442):​n.348+5758G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,018 control chromosomes in the GnomAD database, including 4,872 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 0.23 (4872 hom., cov: 32)
• Consequence: ENSG00000301442 ENST00000778903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543
• Publications: 1 publications found

Genes affected

ENSG00000301442 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778903.1. 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
	ENSG00000301442	ENST00000778903.1		n.348+5758G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35405 AN: 151900 Hom.: 4874 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.233 AC: 35393 AN: 152018 Hom.: 4872 Cov.: 32 AF XY: 0.231 AC XY: 17178 AN XY: 74296

African (AFR) AF: 0.0796 AC: 3302 AN: 41496

American (AMR) AF: 0.224 AC: 3414 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3468

East Asian (EAS) AF: 0.234 AC: 1205 AN: 5154

South Asian (SAS) AF: 0.275 AC: 1326 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2736 AN: 10574

Middle Eastern (MID) AF: 0.345 AC: 100 AN: 290

European-Non Finnish (NFE) AF: 0.314 AC: 21328 AN: 67946

Other (OTH) AF: 0.279 AC: 589 AN: 2108

Alfa AF: 0.256 Hom.: 681

Bravo AF: 0.223

Asia WGS AF: 0.298 AC: 1034 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	13
DANN	Benign	0.64
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs12885270; hg19: chr14-87172830;