16-679831-C-T

Position:

• chr16-679831-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.411 in 145,232 control chromosomes in the GnomAD database, including 12,607 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.41 (12597 hom., cov: 25)
  • Exomes 𝑓: 0.42 (10 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.399

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 16-679831-C-T is Benign according to our data. Variant chr16-679831-C-T is described in ClinVar as [Benign]. Clinvar id is 1231549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 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: 0.411 AC: 59621 AN: 145056 Hom.: 12585 Cov.: 25

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.311

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.364

GnomAD4 exome AF: 0.420 AC: 37 AN: 88 Hom.: 10 AF XY: 0.500 AC XY: 31 AN XY: 62

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.650

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.175

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.411 AC: 59657 AN: 145144 Hom.: 12597 Cov.: 25 AF XY: 0.421 AC XY: 29742 AN XY: 70590

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.371

Alfa AF: 0.244 Hom.: 577

Bravo AF: 0.399

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 25, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12599315; hg19: chr16-729831;