rs2414525

Positions:

• chr15-57935435-G-C

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/exons	MANE	UniProt

Ensembl

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