rs16948563

Variant names:

• chr17-49987777-G-A
• rs16948563

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0762 AC: 3144 AN: 41272

American (AMR) AF: 0.120 AC: 1824 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0584 AC: 202 AN: 3460

East Asian (EAS) AF: 0.173 AC: 883 AN: 5096

South Asian (SAS) AF: 0.128 AC: 613 AN: 4780

European-Finnish (FIN) AF: 0.0626 AC: 660 AN: 10542

Middle Eastern (MID) AF: 0.0734 AC: 21 AN: 286

European-Non Finnish (NFE) AF: 0.0585 AC: 3970 AN: 67820

Other (OTH) AF: 0.0701 AC: 147 AN: 2096

Alfa AF: 0.0663 Hom.: 1602

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
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs16948563; hg19: chr17-48065141;