ENST00000652614.1:n.294+65104G>A

Variant names:

• chr17-54152817-C-T
• rs9303347
• ENST00000652614.1:n.294+65104G>A

Variant summary

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

The ENST00000652614.1(ENSG00000285939):​n.294+65104G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,952 control chromosomes in the GnomAD database, including 3,388 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 0.15 (3388 hom., cov: 32)
• Consequence: ENSG00000285939 ENST00000652614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643
• Publications: 1 publications found

Genes affected

ENSG00000285939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652614.1. 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
	ENSG00000285939	ENST00000652614.1		n.294+65104G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22235 AN: 151834 Hom.: 3369 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.0501

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.147 AC: 22305 AN: 151952 Hom.: 3388 Cov.: 32 AF XY: 0.143 AC XY: 10631 AN XY: 74278

African (AFR) AF: 0.386 AC: 15983 AN: 41412

American (AMR) AF: 0.0917 AC: 1397 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3470

East Asian (EAS) AF: 0.0603 AC: 310 AN: 5140

South Asian (SAS) AF: 0.0502 AC: 242 AN: 4822

European-Finnish (FIN) AF: 0.0355 AC: 377 AN: 10616

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0502 AC: 3411 AN: 67950

Other (OTH) AF: 0.112 AC: 236 AN: 2110

Alfa AF: 0.109 Hom.: 260

Bravo AF: 0.162

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.29
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs9303347; hg19: chr17-52230178;