chr16-23835433-G-C

Variant names:

• chr16-23835433-G-C
• rs2575390

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 0.715 in 152,078 control chromosomes in the GnomAD database, including 39,356 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 0.71 (39356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108664 AN: 151960 Hom.: 39350 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.715 AC: 108709 AN: 152078 Hom.: 39356 Cov.: 32 AF XY: 0.719 AC XY: 53486 AN XY: 74358

African (AFR) AF: 0.617 AC: 25555 AN: 41446

American (AMR) AF: 0.653 AC: 9975 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2668 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4825 AN: 5172

South Asian (SAS) AF: 0.871 AC: 4207 AN: 4830

European-Finnish (FIN) AF: 0.813 AC: 8598 AN: 10574

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50475 AN: 67980

Other (OTH) AF: 0.693 AC: 1466 AN: 2114

Alfa AF: 0.643 Hom.: 1965

Bravo AF: 0.695

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2575390; hg19: chr16-23846754;