rs2069521

Positions:

• chr15-74746626-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 0.0486 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;