rs11648716

chr16-85873010-A-G

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 0.0659 in 152,114 control chromosomes in the GnomAD database, including 354 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 0.066 (354 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0659 AC: 10013 AN: 151996 Hom.: 352 Cov.: 31

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0659 AC: 10028 AN: 152114 Hom.: 354 Cov.: 31 AF XY: 0.0645 AC XY: 4796 AN XY: 74362

Gnomad4 AFR AF: 0.0517

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.0699

Alfa AF: 0.0737 Hom.: 48

Bravo AF: 0.0631

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	16
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11648716; hg19: chr16-85906616;