rs2385525

Variant names:

• chr8-49693050-A-G
• rs2385525

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 0.106 in 152,256 control chromosomes in the GnomAD database, including 913 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 0.11 (913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 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: 0.106 AC: 16190 AN: 152138 Hom.: 912 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.0894

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.106 AC: 16202 AN: 152256 Hom.: 913 Cov.: 33 AF XY: 0.105 AC XY: 7839 AN XY: 74442

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0596

Gnomad4 EAS AF: 0.0900

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0365

Gnomad4 NFE AF: 0.0888

Gnomad4 OTH AF: 0.121

Alfa AF: 0.101 Hom.: 245

Bravo AF: 0.115

Asia WGS AF: 0.143 AC: 499 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2385525; hg19: chr8-50605610;