rs1565496

Variant names:

• chr15-75236841-G-A
• rs1565496

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 0.221 in 152,098 control chromosomes in the GnomAD database, including 3,892 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 0.22 (3892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

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 (SAS) allele frequency at 95% confidence interval = 0.344 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: 0.221 AC: 33626 AN: 151980 Hom.: 3894 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.221 AC: 33635 AN: 152098 Hom.: 3892 Cov.: 32 AF XY: 0.221 AC XY: 16436 AN XY: 74346

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.268

Alfa AF: 0.236 Hom.: 5338

Bravo AF: 0.224

Asia WGS AF: 0.274 AC: 950 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	3.6
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1565496; hg19: chr15-75529182;