16-70081616-G-A

Variant names:

• chr16-70081616-G-A
• rs998109

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0335 AC: 1392 AN: 41496

American (AMR) AF: 0.116 AC: 1770 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3468

East Asian (EAS) AF: 0.139 AC: 718 AN: 5160

South Asian (SAS) AF: 0.220 AC: 1055 AN: 4806

European-Finnish (FIN) AF: 0.119 AC: 1252 AN: 10526

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11403 AN: 67926

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.141 Hom.: 1848

Bravo AF: 0.114

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.28
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs998109; hg19: chr16-70115519;