rs2866619

Variant names:

• chr16-76218244-G-A
• rs2866619

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 0.104 in 152,072 control chromosomes in the GnomAD database, including 1,529 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 (1529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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: 0.104 AC: 15786 AN: 151952 Hom.: 1528 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.104 AC: 15812 AN: 152072 Hom.: 1529 Cov.: 32 AF XY: 0.107 AC XY: 7940 AN XY: 74336

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0539

Gnomad4 NFE AF: 0.0320

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0673 Hom.: 197

Bravo AF: 0.109

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2866619; hg19: chr16-76252142;