16-22957589-T-C

Variant names:

• chr16-22957589-T-C
• rs208600

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 0.801 in 152,104 control chromosomes in the GnomAD database, including 49,136 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 0.80 (49136 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

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 = 0.892 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: 0.801 AC: 121691 AN: 151986 Hom.: 49069 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.801 AC: 121822 AN: 152104 Hom.: 49136 Cov.: 31 AF XY: 0.804 AC XY: 59779 AN XY: 74358

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.789

Alfa AF: 0.774 Hom.: 5709

Bravo AF: 0.807

Asia WGS AF: 0.837 AC: 2913 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	1.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208600; hg19: chr16-22968910;