rs721411

Positions:

• chr17-41492692-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 0.0835 in 247,412 control chromosomes in the GnomAD database, including 1,345 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 0.087 (834 hom., cov: 32)
  • Exomes 𝑓: 0.078 (511 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 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: 0.0869 AC: 13212 AN: 152058 Hom.: 831 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0907

GnomAD4 exome AF: 0.0779 AC: 7421 AN: 95234 Hom.: 511 AF XY: 0.0829 AC XY: 4151 AN XY: 50102

Gnomad4 AFR exome AF: 0.0968

Gnomad4 AMR exome AF: 0.223

Gnomad4 ASJ exome AF: 0.0382

Gnomad4 EAS exome AF: 0.216

Gnomad4 SAS exome AF: 0.114

Gnomad4 FIN exome AF: 0.0414

Gnomad4 NFE exome AF: 0.0445

Gnomad4 OTH exome AF: 0.0577

GnomAD4 genome AF: 0.0870 AC: 13236 AN: 152178 Hom.: 834 Cov.: 32 AF XY: 0.0900 AC XY: 6695 AN XY: 74404

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0473

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0898

Alfa AF: 0.0715 Hom.: 319

Bravo AF: 0.101

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721411; hg19: chr17-39648944;