rs939394

Variant names:

• chr15-45975700-A-T
• rs939394

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 0.337 in 152,042 control chromosomes in the GnomAD database, including 11,129 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 0.34 (11129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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: 0.337 AC: 51227 AN: 151922 Hom.: 11096 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.337 AC: 51302 AN: 152042 Hom.: 11129 Cov.: 32 AF XY: 0.332 AC XY: 24681 AN XY: 74334

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.278

Alfa AF: 0.316 Hom.: 1146

Bravo AF: 0.341

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs939394; hg19: chr15-46267898;