chr15-57935435-G-C

Variant names:

• chr15-57935435-G-C
• rs2414525

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.177 AC: 7350 AN: 41466

American (AMR) AF: 0.109 AC: 1662 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0626 AC: 217 AN: 3466

East Asian (EAS) AF: 0.168 AC: 869 AN: 5184

South Asian (SAS) AF: 0.107 AC: 515 AN: 4824

European-Finnish (FIN) AF: 0.0805 AC: 854 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0741 AC: 5034 AN: 67970

Other (OTH) AF: 0.105 AC: 221 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.19
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2414525; hg19: chr15-58227633;