rs2069521

Variant names:

• chr15-74746626-G-A
• rs2069521

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 0.0486 in 152,278 control chromosomes in the GnomAD database, including 267 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 0.049 (267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0909 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: 0.0486 AC: 7397 AN: 152160 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0486 AC: 7395 AN: 152278 Hom.: 267 Cov.: 32 AF XY: 0.0498 AC XY: 3707 AN XY: 74454

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.0735

Gnomad4 SAS AF: 0.0857

Gnomad4 FIN AF: 0.0375

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0384 Hom.: 18

Bravo AF: 0.0487

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069521; hg19: chr15-75038967;