ENST00000825469.1:n.320+8327G>A

Variant names:

• chr12-27819417-G-A
• rs9988960
• ENST00000825469.1:n.320+8327G>A

Variant summary

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

The ENST00000825469.1(ENSG00000257042):​n.320+8327G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,008 control chromosomes in the GnomAD database, including 11,539 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 0.39 (11539 hom., cov: 32)
• Consequence: ENSG00000257042 ENST00000825469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 8 publications found

Genes affected

ENSG00000257042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825469.1. 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
	ENSG00000257042	ENST00000825469.1		n.320+8327G>A		intron	N/A
	ENSG00000257042	ENST00000825470.1		n.175+8327G>A		intron	N/A
	ENSG00000257042	ENST00000825471.1		n.140+8327G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58933 AN: 151892 Hom.: 11540 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.388 AC: 58964 AN: 152008 Hom.: 11539 Cov.: 32 AF XY: 0.388 AC XY: 28818 AN XY: 74280

African (AFR) AF: 0.391 AC: 16221 AN: 41472

American (AMR) AF: 0.349 AC: 5334 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1530 AN: 5150

South Asian (SAS) AF: 0.457 AC: 2198 AN: 4808

European-Finnish (FIN) AF: 0.376 AC: 3958 AN: 10528

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27016 AN: 67992

Other (OTH) AF: 0.379 AC: 799 AN: 2110

Alfa AF: 0.388 Hom.: 49952

Bravo AF: 0.380

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.34
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs9988960; hg19: chr12-27972350;