rs16948563

chr17-49987777-G-A

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 0.0757 in 151,514 control chromosomes in the GnomAD database, including 525 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 0.076 (525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.164 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: 0.0757 AC: 11453 AN: 151394 Hom.: 523 Cov.: 32

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.00221

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0584

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0714

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0704

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

GnomAD4 genome AF: 0.0757 AC: 11466 AN: 151514 Hom.: 525 Cov.: 32 AF XY: 0.0793 AC XY: 5871 AN XY: 74042

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0584

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0585

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0624 Hom.: 571

Bravo AF: 0.0807

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.3
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16948563; hg19: chr17-48065141;