rs998109

Variant names:

• chr16-70081616-G-A
• rs998109

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 0.121 in 151,962 control chromosomes in the GnomAD database, including 1,395 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 0.12 (1395 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 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: 0.121 AC: 18358 AN: 151842 Hom.: 1395 Cov.: 31

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.121 AC: 18357 AN: 151962 Hom.: 1395 Cov.: 31 AF XY: 0.120 AC XY: 8943 AN XY: 74268

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.143

Alfa AF: 0.152 Hom.: 1303

Bravo AF: 0.114

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs998109; hg19: chr16-70115519;