rs17287745

chr5-143275450-A-G

Variant summary

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

The variant allele was found at a frequency of 0.31 in 152,062 control chromosomes in the GnomAD database, including 8,397 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 0.31 (8397 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47098 AN: 151946 Hom.: 8399 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.310 AC: 47096 AN: 152062 Hom.: 8397 Cov.: 31 AF XY: 0.305 AC XY: 22633 AN XY: 74312

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.331

Alfa AF: 0.388 Hom.: 12206

Bravo AF: 0.303

Asia WGS AF: 0.277 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.4
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: rs17287745; hg19: chr5-142655015; COSMIC: COSV59429544;