rs17284960

Variant names:

• chr5-164196496-C-T
• rs17284960
• ENST00000521805.1:n.284-2140G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521805.1(ENSG00000253331):​n.284-2140G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,916 control chromosomes in the GnomAD database, including 9,011 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 0.33 (9011 hom., cov: 32)
• Consequence: ENSG00000253331 ENST00000521805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587

Genes affected

ENSG00000253331 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 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
ENSG00000253331	ENST00000521805.1	n.284-2140G>A		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50372 AN: 151798 Hom.: 9002 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.332 AC: 50406 AN: 151916 Hom.: 9011 Cov.: 32 AF XY: 0.336 AC XY: 24943 AN XY: 74226

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.350

Alfa AF: 0.353 Hom.: 4525

Bravo AF: 0.324

Asia WGS AF: 0.306 AC: 1060 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17284960; hg19: chr5-163623502;