16-59347691-A-G

Variant names:

• chr16-59347691-A-G
• rs17258206

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 0.0752 in 152,080 control chromosomes in the GnomAD database, including 922 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 0.075 (922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 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: 0.0752 AC: 11430 AN: 151962 Hom.: 923 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0236

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0752 AC: 11439 AN: 152080 Hom.: 922 Cov.: 32 AF XY: 0.0803 AC XY: 5967 AN XY: 74344

African (AFR) AF: 0.118 AC: 4914 AN: 41474

American (AMR) AF: 0.0589 AC: 899 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2054 AN: 5156

South Asian (SAS) AF: 0.227 AC: 1093 AN: 4822

European-Finnish (FIN) AF: 0.0399 AC: 422 AN: 10588

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0236 AC: 1608 AN: 67998

Other (OTH) AF: 0.0775 AC: 163 AN: 2104

Alfa AF: 0.0541 Hom.: 86

Bravo AF: 0.0782

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.037
DANN	Benign	0.82
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs17258206; hg19: chr16-59381595;