rs2729409

Positions:

• chr18-30561722-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.281

Alfa AF: 0.237 Hom.: 6762

Bravo AF: 0.316

Asia WGS AF: 0.240 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2729409; hg19: chr18-28141688;