rs2414525

Variant names:

• chr15-57935435-G-C
• rs2414525

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 0.111 in 152,096 control chromosomes in the GnomAD database, including 1,112 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 (1112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.110 AC: 16789 AN: 151976 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.111 AC: 16809 AN: 152096 Hom.: 1112 Cov.: 32 AF XY: 0.112 AC XY: 8329 AN XY: 74370

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0626

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0741

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0853 Hom.: 94

Bravo AF: 0.117

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2414525; hg19: chr15-58227633;