rs16996381

Variant names:

• chr22-36115231-G-A
• rs16996381

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 0.299 in 152,032 control chromosomes in the GnomAD database, including 9,871 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 0.30 (9871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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: 0.299 AC: 45441 AN: 151914 Hom.: 9847 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.299 AC: 45504 AN: 152032 Hom.: 9871 Cov.: 32 AF XY: 0.294 AC XY: 21872 AN XY: 74312

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.243

Alfa AF: 0.225 Hom.: 1297

Bravo AF: 0.319

Asia WGS AF: 0.207 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16996381; hg19: chr22-36511279;