rs353739

Variant names:

• chr8-56790300-G-A
• rs353739

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 0.162 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0883 AC: 3654 AN: 41404

American (AMR) AF: 0.269 AC: 4104 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3468

East Asian (EAS) AF: 0.0689 AC: 356 AN: 5164

South Asian (SAS) AF: 0.197 AC: 944 AN: 4788

European-Finnish (FIN) AF: 0.157 AC: 1636 AN: 10426

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12619 AN: 67894

Other (OTH) AF: 0.159 AC: 335 AN: 2108

Alfa AF: 0.166 Hom.: 313

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
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs353739; hg19: chr8-57702859;