chr16-60699699-C-T

Variant names:

• chr16-60699699-C-T
• rs17822114

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 0.0355 in 151,754 control chromosomes in the GnomAD database, including 163 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 0.035 (163 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.0937 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: 0.0355 AC: 5381 AN: 151636 Hom.: 164 Cov.: 30

Gnomad AFR AF: 0.00712

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.00837

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0365

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

GnomAD4 genome AF: 0.0355 AC: 5387 AN: 151754 Hom.: 163 Cov.: 30 AF XY: 0.0389 AC XY: 2881 AN XY: 74102

African (AFR) AF: 0.00710 AC: 294 AN: 41412

American (AMR) AF: 0.0863 AC: 1313 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.00837 AC: 29 AN: 3466

East Asian (EAS) AF: 0.0487 AC: 250 AN: 5132

South Asian (SAS) AF: 0.101 AC: 486 AN: 4804

European-Finnish (FIN) AF: 0.0569 AC: 594 AN: 10444

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0344 AC: 2338 AN: 67978

Other (OTH) AF: 0.0361 AC: 76 AN: 2106

Alfa AF: 0.0346 Hom.: 235

Bravo AF: 0.0357

Asia WGS AF: 0.0680 AC: 239 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	7.2
DANN	Benign	0.64
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs17822114; hg19: chr16-60733603;