chr3-16799306-C-T

Variant names:

• chr3-16799306-C-T
• rs1449531

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 0.0746 in 152,182 control chromosomes in the GnomAD database, including 497 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 0.075 (497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 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: 0.0746 AC: 11341 AN: 152064 Hom.: 499 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0746 AC: 11346 AN: 152182 Hom.: 497 Cov.: 32 AF XY: 0.0744 AC XY: 5531 AN XY: 74384

African (AFR) AF: 0.0773 AC: 3209 AN: 41512

American (AMR) AF: 0.0725 AC: 1108 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1126 AN: 5170

South Asian (SAS) AF: 0.0535 AC: 258 AN: 4826

European-Finnish (FIN) AF: 0.0594 AC: 630 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4476 AN: 68004

Other (OTH) AF: 0.0658 AC: 139 AN: 2112

Alfa AF: 0.0687 Hom.: 688

Bravo AF: 0.0804

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.18
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs1449531; hg19: chr3-16840813;