rs16955339

Variant names:

• chr17-54893699-G-T
• rs16955339

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 0.0369 in 152,264 control chromosomes in the GnomAD database, including 141 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 0.037 (141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.144 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: 0.0369 AC: 5608 AN: 152144 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0205

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0316

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0369 AC: 5616 AN: 152264 Hom.: 141 Cov.: 32 AF XY: 0.0384 AC XY: 2860 AN XY: 74468

African (AFR) AF: 0.0388 AC: 1614 AN: 41560

American (AMR) AF: 0.0205 AC: 314 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3472

East Asian (EAS) AF: 0.153 AC: 790 AN: 5174

South Asian (SAS) AF: 0.0566 AC: 273 AN: 4826

European-Finnish (FIN) AF: 0.0284 AC: 302 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0316 AC: 2152 AN: 68002

Other (OTH) AF: 0.0298 AC: 63 AN: 2114

Alfa AF: 0.0353 Hom.: 98

Bravo AF: 0.0367

Asia WGS AF: 0.100 AC: 346 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	2.5
DANN	Benign	0.51
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs16955339; hg19: chr17-52971060;