16-79618644-C-T

Variant names:

• chr16-79618644-C-T
• rs386965

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 0.713 in 152,110 control chromosomes in the GnomAD database, including 39,305 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 0.71 (39305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664

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 (NFE) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108447 AN: 151992 Hom.: 39273 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.713 AC: 108527 AN: 152110 Hom.: 39305 Cov.: 32 AF XY: 0.709 AC XY: 52753 AN XY: 74380

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.721

Alfa AF: 0.756 Hom.: 51132

Bravo AF: 0.698

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386965; hg19: chr16-79652541;