16-55139182-G-A

Position:

• chr16-55139182-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0468 in 152,314 control chromosomes in the GnomAD database, including 220 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 0.047 (220 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0467 AC: 7115 AN: 152196 Hom.: 221 Cov.: 33

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0691

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0468 AC: 7123 AN: 152314 Hom.: 220 Cov.: 33 AF XY: 0.0462 AC XY: 3439 AN XY: 74480

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.00484

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0691

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0525 Hom.: 309

Bravo AF: 0.0401

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17210989; hg19: chr16-55173094;