rs1565863

Variant names:

• chr15-40145919-G-A
• rs1565863

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;