rs16963477

chr15-50238218-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 0.0656 in 152,290 control chromosomes in the GnomAD database, including 624 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 0.066 (624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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: 0.0655 AC: 9966 AN: 152172 Hom.: 621 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.00910

Gnomad FIN AF: 0.00847

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0274

Gnomad OTH AF: 0.0487

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

GnomAD4 genome AF: 0.0656 AC: 9988 AN: 152290 Hom.: 624 Cov.: 32 AF XY: 0.0621 AC XY: 4623 AN XY: 74490

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0293

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.00890

Gnomad4 FIN AF: 0.00847

Gnomad4 NFE AF: 0.0274

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0361 Hom.: 180

Bravo AF: 0.0723

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.8
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16963477; hg19: chr15-50530415;