rs1565863

chr15-40145919-G-A

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 0.563 in 152,080 control chromosomes in the GnomAD database, including 26,339 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 0.56 (26339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 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: 0.563 AC: 85565 AN: 151962 Hom.: 26335 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.563 AC: 85599 AN: 152080 Hom.: 26339 Cov.: 32 AF XY: 0.560 AC XY: 41628 AN XY: 74340

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.537

Alfa AF: 0.670 Hom.: 56093

Bravo AF: 0.542

Asia WGS AF: 0.381 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.44
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1565863; hg19: chr15-40438120;