rs1384565

Variant names:

• chr15-101264707-T-C
• rs1384565

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;