rs250567

chr16-23383078-C-T

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 0.0811 in 152,246 control chromosomes in the GnomAD database, including 589 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 0.081 (589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12328 AN: 152128 Hom.: 587 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.0806

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0811 AC: 12352 AN: 152246 Hom.: 589 Cov.: 32 AF XY: 0.0819 AC XY: 6100 AN XY: 74438

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0707

Gnomad4 FIN AF: 0.0806

Gnomad4 NFE AF: 0.0590

Gnomad4 OTH AF: 0.0846

Alfa AF: 0.0651 Hom.: 369

Bravo AF: 0.0828

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.34
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: rs250567; hg19: chr16-23394399;