16-68737219-A-C

Position:

• chr16-68737219-A-C

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 0.0117 in 574,956 control chromosomes in the GnomAD database, including 305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.011 (89 hom., cov: 33)
  • Exomes 𝑓: 0.012 (216 hom.)
• Consequence: Unknown
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 16-68737219-A-C is Benign according to our data. Variant chr16-68737219-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 676637.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 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: 0.0109 AC: 1657 AN: 151802 Hom.: 90 Cov.: 33

Gnomad AFR AF: 0.00293

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.00833

Gnomad FIN AF: 0.00265

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000707

Gnomad OTH AF: 0.0148

GnomAD4 exome AF: 0.0120 AC: 5063 AN: 423036 Hom.: 216 Cov.: 4 AF XY: 0.0111 AC XY: 2480 AN XY: 222822

Gnomad4 AFR exome AF: 0.00227

Gnomad4 AMR exome AF: 0.0708

Gnomad4 ASJ exome AF: 0.00450

Gnomad4 EAS exome AF: 0.110

Gnomad4 SAS exome AF: 0.00652

Gnomad4 FIN exome AF: 0.00256

Gnomad4 NFE exome AF: 0.000683

Gnomad4 OTH exome AF: 0.0112

GnomAD4 genome AF: 0.0109 AC: 1657 AN: 151920 Hom.: 89 Cov.: 33 AF XY: 0.0118 AC XY: 878 AN XY: 74266

Gnomad4 AFR AF: 0.00292

Gnomad4 AMR AF: 0.0464

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.00834

Gnomad4 FIN AF: 0.00265

Gnomad4 NFE AF: 0.000707

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.00139 Hom.: 0

Bravo AF: 0.0166

Asia WGS AF: 0.0680 AC: 236 AN: 3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 17, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	8.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28372783; hg19: chr16-68771122;