rs16963477

Variant names:

• chr15-50238218-A-G
• rs16963477

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 0.0656 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.164 AC: 6817 AN: 41526

American (AMR) AF: 0.0293 AC: 449 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3470

East Asian (EAS) AF: 0.0970 AC: 503 AN: 5184

South Asian (SAS) AF: 0.00890 AC: 43 AN: 4832

European-Finnish (FIN) AF: 0.00847 AC: 90 AN: 10624

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0274 AC: 1863 AN: 68032

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0411 Hom.: 329

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
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs16963477; hg19: chr15-50530415;