rs2385525

Positions:

• chr8-49693050-A-G

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/exons	MANE	UniProt

Ensembl

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