chr3-23699547-A-G

Variant names:

• chr3-23699547-A-G
• rs9833833

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 0.453 in 151,928 control chromosomes in the GnomAD database, including 16,623 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 0.45 (16623 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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: 0.453 AC: 68831 AN: 151810 Hom.: 16618 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.453 AC: 68890 AN: 151928 Hom.: 16623 Cov.: 31 AF XY: 0.462 AC XY: 34292 AN XY: 74264

African (AFR) AF: 0.557 AC: 23069 AN: 41416

American (AMR) AF: 0.480 AC: 7329 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3464

East Asian (EAS) AF: 0.718 AC: 3715 AN: 5172

South Asian (SAS) AF: 0.682 AC: 3275 AN: 4804

European-Finnish (FIN) AF: 0.414 AC: 4369 AN: 10560

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24520 AN: 67936

Other (OTH) AF: 0.419 AC: 884 AN: 2110

Alfa AF: 0.388 Hom.: 13741

Bravo AF: 0.456

Asia WGS AF: 0.667 AC: 2319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.49
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs9833833; hg19: chr3-23741038;