rs2608200

Variant names:

• chr16-20110968-A-G
• rs2608200

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 0.79 in 152,074 control chromosomes in the GnomAD database, including 47,722 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 0.79 (47722 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.790 AC: 120006 AN: 151954 Hom.: 47669 Cov.: 30

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.790 AC: 120117 AN: 152074 Hom.: 47722 Cov.: 30 AF XY: 0.788 AC XY: 58576 AN XY: 74338

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.797

Alfa AF: 0.771 Hom.: 7821

Bravo AF: 0.795

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2608200; hg19: chr16-20122290;