chr16-54460512-A-G

Position:

• chr16-54460512-A-G

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 0.767 in 152,192 control chromosomes in the GnomAD database, including 44,974 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 0.77 (44974 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 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: 0.767 AC: 116616 AN: 152074 Hom.: 44944 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.767 AC: 116696 AN: 152192 Hom.: 44974 Cov.: 33 AF XY: 0.773 AC XY: 57533 AN XY: 74402

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.764

Alfa AF: 0.774 Hom.: 61836

Bravo AF: 0.758

Asia WGS AF: 0.855 AC: 2971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.052
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9921518; hg19: chr16-54494424;