16-69553218-T-C

Variant names:

• chr16-69553218-T-C
• rs17230557

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 0.0593 in 152,270 control chromosomes in the GnomAD database, including 294 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 0.059 (294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0717 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: 0.0592 AC: 9014 AN: 152152 Hom.: 292 Cov.: 32

Gnomad AFR AF: 0.0444

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0593 AC: 9026 AN: 152270 Hom.: 294 Cov.: 32 AF XY: 0.0580 AC XY: 4315 AN XY: 74454

African (AFR) AF: 0.0446 AC: 1855 AN: 41550

American (AMR) AF: 0.0518 AC: 791 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4828

European-Finnish (FIN) AF: 0.0686 AC: 728 AN: 10608

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4993 AN: 68020

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0600 Hom.: 38

Bravo AF: 0.0592

Asia WGS AF: 0.0180 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.30
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs17230557; hg19: chr16-69587121;