rs16938215

Variant names:

• chr8-72446353-C-T
• rs16938215

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 0.0865 in 151,928 control chromosomes in the GnomAD database, including 720 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 0.087 (720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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: 0.0866 AC: 13150 AN: 151814 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0875

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.0865 AC: 13143 AN: 151928 Hom.: 720 Cov.: 32 AF XY: 0.0877 AC XY: 6505 AN XY: 74212

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.0427

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0707

Gnomad4 FIN AF: 0.0930

Gnomad4 NFE AF: 0.0875

Gnomad4 OTH AF: 0.0977

Alfa AF: 0.0845 Hom.: 594

Bravo AF: 0.0910

Asia WGS AF: 0.119 AC: 416 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16938215; hg19: chr8-73358588;