chr16-65796106-T-C

Position:

• chr16-65796106-T-C

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 0.778 in 152,048 control chromosomes in the GnomAD database, including 46,749 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 0.78 (46749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.778 AC: 118197 AN: 151930 Hom.: 46691 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.778 AC: 118324 AN: 152048 Hom.: 46749 Cov.: 31 AF XY: 0.783 AC XY: 58155 AN XY: 74314

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.769

Alfa AF: 0.756 Hom.: 5961

Bravo AF: 0.784

Asia WGS AF: 0.905 AC: 3146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.92
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs468905; hg19: chr16-65830009;