15-45022396-C-G

Variant names:

• chr15-45022396-C-G
• rs3759890

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 0.194 in 152,028 control chromosomes in the GnomAD database, including 3,425 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 0.19 (3425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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: 0.194 AC: 29476 AN: 151910 Hom.: 3407 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0713

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.194 AC: 29543 AN: 152028 Hom.: 3425 Cov.: 32 AF XY: 0.197 AC XY: 14641 AN XY: 74274

African (AFR) AF: 0.305 AC: 12616 AN: 41426

American (AMR) AF: 0.204 AC: 3127 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0713 AC: 247 AN: 3462

East Asian (EAS) AF: 0.322 AC: 1655 AN: 5146

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2006 AN: 10568

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8268 AN: 67998

Other (OTH) AF: 0.186 AC: 393 AN: 2110

Alfa AF: 0.0648 Hom.: 63

Bravo AF: 0.202

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs3759890; hg19: chr15-45314594;