rs42309

Variant names:

• chr16-9319747-G-T
• rs42309

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 0.415 in 152,114 control chromosomes in the GnomAD database, including 13,734 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 0.41 (13734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 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: 0.415 AC: 63055 AN: 151996 Hom.: 13739 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.415 AC: 63060 AN: 152114 Hom.: 13734 Cov.: 32 AF XY: 0.414 AC XY: 30752 AN XY: 74338

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.410

Alfa AF: 0.459 Hom.: 3357

Bravo AF: 0.397

Asia WGS AF: 0.317 AC: 1105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.44
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs42309; hg19: chr16-9413604;