rs16975343

Variant names:

• chr16-22993770-G-T
• rs16975343

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 0.0841 in 152,178 control chromosomes in the GnomAD database, including 675 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 0.084 (675 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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: 0.0838 AC: 12745 AN: 152060 Hom.: 658 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0735

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0841 AC: 12799 AN: 152178 Hom.: 675 Cov.: 31 AF XY: 0.0838 AC XY: 6237 AN XY: 74400

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0473

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0735

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0740 Hom.: 235

Bravo AF: 0.0813

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16975343; hg19: chr16-23005091;