rs17822114

Positions:

• chr16-60699699-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 0.0355 in 151,754 control chromosomes in the GnomAD database, including 163 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 0.035 (163 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0937 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

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5381 AN: 151636 Hom.: 164 Cov.: 30

Gnomad AFR AF: 0.00712

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.00837

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0365

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

GnomAD4 genome AF: 0.0355 AC: 5387 AN: 151754 Hom.: 163 Cov.: 30 AF XY: 0.0389 AC XY: 2881 AN XY: 74102

Gnomad4 AFR AF: 0.00710

Gnomad4 AMR AF: 0.0863

Gnomad4 ASJ AF: 0.00837

Gnomad4 EAS AF: 0.0487

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0361

Alfa AF: 0.0386 Hom.: 106

Bravo AF: 0.0357

Asia WGS AF: 0.0680 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17822114; hg19: chr16-60733603;