ENST00000732215.1:n.169+27399C>A

Variant names:

• chr3-120526978-C-A
• rs1259489
• ENST00000732215.1:n.169+27399C>A

Variant summary

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

The ENST00000732215.1(ENSG00000286735):​n.169+27399C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,084 control chromosomes in the GnomAD database, including 4,452 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 0.24 (4452 hom., cov: 32)
• Consequence: ENSG00000286735 ENST00000732215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 1 publications found

Genes affected

ENSG00000286735 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732215.1. 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
	ENSG00000286735	ENST00000732215.1		n.169+27399C>A		intron	N/A
	ENSG00000286735	ENST00000732216.1		n.247-20207C>A		intron	N/A
	ENSG00000295741	ENST00000732308.1		n.127+33828G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36234 AN: 151966 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.239 AC: 36278 AN: 152084 Hom.: 4452 Cov.: 32 AF XY: 0.235 AC XY: 17460 AN XY: 74332

African (AFR) AF: 0.241 AC: 10001 AN: 41482

American (AMR) AF: 0.196 AC: 3003 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3468

East Asian (EAS) AF: 0.0510 AC: 264 AN: 5172

South Asian (SAS) AF: 0.234 AC: 1128 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2092 AN: 10564

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17710 AN: 67968

Other (OTH) AF: 0.261 AC: 551 AN: 2108

Alfa AF: 0.188 Hom.: 583

Bravo AF: 0.237

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.32
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs1259489; hg19: chr3-120245825;