rs998109

Positions:

• chr16-70081616-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;