rs2729409

Variant names:

• chr18-30561722-G-A
• rs2729409

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 0.304 in 151,856 control chromosomes in the GnomAD database, including 8,184 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 0.30 (8184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.304 AC: 46068 AN: 151738 Hom.: 8153 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.304 AC: 46154 AN: 151856 Hom.: 8184 Cov.: 32 AF XY: 0.301 AC XY: 22349 AN XY: 74242

African (AFR) AF: 0.503 AC: 20869 AN: 41468

American (AMR) AF: 0.236 AC: 3606 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 760 AN: 3456

East Asian (EAS) AF: 0.257 AC: 1328 AN: 5168

South Asian (SAS) AF: 0.180 AC: 868 AN: 4814

European-Finnish (FIN) AF: 0.231 AC: 2441 AN: 10582

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15431 AN: 67806

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.250 Hom.: 10895

Bravo AF: 0.316

Asia WGS AF: 0.240 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.30
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2729409; hg19: chr18-28141688;