rs3825786

Positions:

• chr15-42138944-A-G

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 0.164 in 152,016 control chromosomes in the GnomAD database, including 2,536 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 (2536 hom., cov: 33)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 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: 0.164 AC: 24850 AN: 151878 Hom.: 2532 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.137

GnomAD4 exome AF: 0.200 AC: 4 AN: 20 Hom.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.164 AC: 24881 AN: 151996 Hom.: 2536 Cov.: 33 AF XY: 0.165 AC XY: 12246 AN XY: 74318

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.0966

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.0971

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.136

Alfa AF: 0.122 Hom.: 2724

Bravo AF: 0.163

Asia WGS AF: 0.313 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3825786; hg19: chr15-42431142;