rs11648716

Variant names:

• chr16-85873010-A-G
• rs11648716

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 0.0659 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0517 AC: 2143 AN: 41484

American (AMR) AF: 0.0485 AC: 742 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.119 AC: 572 AN: 4818

European-Finnish (FIN) AF: 0.0421 AC: 445 AN: 10578

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5458 AN: 67970

Other (OTH) AF: 0.0699 AC: 148 AN: 2116

Alfa AF: 0.0651 Hom.: 181

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
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs11648716; hg19: chr16-85906616;