rs2216755

Variant names:

• chr16-60780857-C-A
• rs2216755

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 0.153 in 151,900 control chromosomes in the GnomAD database, including 2,032 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 0.15 (2032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.277 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: 0.153 AC: 23222 AN: 151782 Hom.: 2030 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23239 AN: 151900 Hom.: 2032 Cov.: 32 AF XY: 0.154 AC XY: 11466 AN XY: 74230

African (AFR) AF: 0.189 AC: 7829 AN: 41440

American (AMR) AF: 0.284 AC: 4337 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3464

East Asian (EAS) AF: 0.197 AC: 1011 AN: 5144

South Asian (SAS) AF: 0.118 AC: 569 AN: 4824

European-Finnish (FIN) AF: 0.0921 AC: 974 AN: 10574

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7493 AN: 67884

Other (OTH) AF: 0.150 AC: 316 AN: 2108

Alfa AF: 0.137 Hom.: 204

Bravo AF: 0.172

Asia WGS AF: 0.150 AC: 523 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.46
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2216755; hg19: chr16-60814761;