chr16-23383078-C-T

Variant names:

• chr16-23383078-C-T
• rs250567

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 0.0811 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.124 AC: 5161 AN: 41534

American (AMR) AF: 0.0672 AC: 1028 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3470

East Asian (EAS) AF: 0.113 AC: 585 AN: 5178

South Asian (SAS) AF: 0.0707 AC: 341 AN: 4820

European-Finnish (FIN) AF: 0.0806 AC: 855 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0590 AC: 4015 AN: 68024

Other (OTH) AF: 0.0846 AC: 179 AN: 2116

Alfa AF: 0.0685 Hom.: 629

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs250567; hg19: chr16-23394399;