chr16-60659050-C-T

Position:

• chr16-60659050-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 0.788 in 152,126 control chromosomes in the GnomAD database, including 47,363 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 0.79 (47363 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119849 AN: 152008 Hom.: 47335 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.788 AC: 119930 AN: 152126 Hom.: 47363 Cov.: 31 AF XY: 0.788 AC XY: 58614 AN XY: 74378

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.779

Alfa AF: 0.799 Hom.: 6070

Bravo AF: 0.785

Asia WGS AF: 0.688 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.039
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544806; hg19: chr16-60692954;