rs9303347

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285939 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285939	ENST00000652614.1	n.294+65104G>A		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.0502

Gnomad4 FIN AF: 0.0355

Gnomad4 NFE AF: 0.0502

Gnomad4 OTH AF: 0.112

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9303347; hg19: chr17-52230178;