rs16963477

Variant names:

• chr15-50238218-A-G
• rs16963477

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;