rs6496669

chr15-90352033-G-A

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 0.229 in 152,178 control chromosomes in the GnomAD database, including 4,350 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 0.23 (4350 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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: 0.229 AC: 34855 AN: 152060 Hom.: 4341 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.229 AC: 34884 AN: 152178 Hom.: 4350 Cov.: 33 AF XY: 0.228 AC XY: 16950 AN XY: 74400

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.220

Alfa AF: 0.201 Hom.: 5550

Bravo AF: 0.229

Asia WGS AF: 0.250 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6496669; hg19: chr15-90895265;