rs17006293

chr3-69645755-C-T

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 0.0472 in 152,230 control chromosomes in the GnomAD database, including 372 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 0.047 (372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 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: 0.0472 AC: 7176 AN: 152112 Hom.: 371 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0472 AC: 7184 AN: 152230 Hom.: 372 Cov.: 32 AF XY: 0.0510 AC XY: 3793 AN XY: 74420

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0529

Alfa AF: 0.0443 Hom.: 247

Bravo AF: 0.0512

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.7
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17006293; hg19: chr3-69694906;