rs10459815

Positions:

• chr16-50684890-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 0.0329 in 152,200 control chromosomes in the GnomAD database, including 187 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 0.033 (187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.117 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: 0.0329 AC: 4997 AN: 152082 Hom.: 187 Cov.: 32

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00378

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0329 AC: 5006 AN: 152200 Hom.: 187 Cov.: 32 AF XY: 0.0336 AC XY: 2500 AN XY: 74406

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.0561

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.00954

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.00378

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.00978 Hom.: 33

Bravo AF: 0.0383

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.011
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10459815; hg19: chr16-50718801;