rs9303347

Positions:

• chr17-54152817-C-T

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, non coding transcript 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: ENST00000652614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652614.1	n.294+65104G>A		intron_variant, non_coding_transcript_variant

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;