17-14572284-C-T

Variant names:

• chr17-14572284-C-T
• rs2058237
• ENST00000791247.1:n.321+3522G>A

Variant summary

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

The ENST00000791247.1(ENSG00000303027):​n.321+3522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,950 control chromosomes in the GnomAD database, including 14,093 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 0.42 (14093 hom., cov: 33)
• Consequence: ENSG00000303027 ENST00000791247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 6 publications found

Genes affected

ENSG00000303027 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791247.1. 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
	ENSG00000303027	ENST00000791247.1		n.321+3522G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63955 AN: 151832 Hom.: 14089 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.421 AC: 63982 AN: 151950 Hom.: 14093 Cov.: 33 AF XY: 0.420 AC XY: 31175 AN XY: 74254

African (AFR) AF: 0.298 AC: 12369 AN: 41472

American (AMR) AF: 0.508 AC: 7753 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3195 AN: 5158

South Asian (SAS) AF: 0.426 AC: 2047 AN: 4810

European-Finnish (FIN) AF: 0.407 AC: 4298 AN: 10550

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31409 AN: 67922

Other (OTH) AF: 0.446 AC: 941 AN: 2112

Alfa AF: 0.445 Hom.: 32894

Bravo AF: 0.429

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.27
PhyloP100		-1.1

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: rs2058237;

hg19: chr17-14475601;