rs353739

chr8-56790300-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 0.162 in 151,692 control chromosomes in the GnomAD database, including 2,292 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 0.16 (2292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24524 AN: 151574 Hom.: 2293 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.162 AC: 24542 AN: 151692 Hom.: 2292 Cov.: 32 AF XY: 0.161 AC XY: 11938 AN XY: 74140

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0689

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.159

Alfa AF: 0.169 Hom.: 312

Bravo AF: 0.170

Asia WGS AF: 0.143 AC: 496 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.0
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353739; hg19: chr8-57702859;