rs1384565

chr15-101264707-T-C

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 0.0412 in 152,252 control chromosomes in the GnomAD database, including 384 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 0.041 (384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 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: 0.0411 AC: 6248 AN: 152134 Hom.: 378 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0412 AC: 6278 AN: 152252 Hom.: 384 Cov.: 32 AF XY: 0.0453 AC XY: 3373 AN XY: 74436

Gnomad4 AFR AF: 0.0342

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.0360

Gnomad4 FIN AF: 0.0395

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0423 Hom.: 150

Bravo AF: 0.0510

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.14
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1384565; hg19: chr15-101804912;