16-85959043-C-T

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 0.555 in 151,650 control chromosomes in the GnomAD database, including 23,912 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 0.55 (23912 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.555 AC: 84059 AN: 151532 Hom.: 23915 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.555 AC: 84091 AN: 151650 Hom.: 23912 Cov.: 31 AF XY: 0.562 AC XY: 41620 AN XY: 74042

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.572

Alfa AF: 0.520 Hom.: 19491

Bravo AF: 0.568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.3
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12444486; hg19: chr16-85992649;