rs9928199

chr16-77057714-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 0.103 in 145,186 control chromosomes in the GnomAD database, including 2,489 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 0.10 (2489 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 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: 0.103 AC: 14966 AN: 145064 Hom.: 2478 Cov.: 29

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0388

Gnomad EAS AF: 0.00219

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.103 AC: 14996 AN: 145186 Hom.: 2489 Cov.: 29 AF XY: 0.103 AC XY: 7284 AN XY: 70680

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0388

Gnomad4 EAS AF: 0.00219

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.0968

Alfa AF: 0.0907 Hom.: 1485

Asia WGS AF: 0.0820 AC: 280 AN: 3382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.6
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9928199; hg19: chr16-77091611;