rs16989370

Variant names:

• chr20-40847942-C-T
• rs16989370

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 0.0305 in 152,232 control chromosomes in the GnomAD database, including 156 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 0.030 (156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 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: 0.0305 AC: 4642 AN: 152114 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0228

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0305 AC: 4641 AN: 152232 Hom.: 156 Cov.: 32 AF XY: 0.0306 AC XY: 2281 AN XY: 74446

Gnomad4 AFR AF: 0.0305

Gnomad4 AMR AF: 0.0184

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.0203

Gnomad4 NFE AF: 0.0228

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0254 Hom.: 13

Bravo AF: 0.0318

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16989370; hg19: chr20-39476582;