rs2011732

Positions:

• chr17-63919139-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.219 in 152,124 control chromosomes in the GnomAD database, including 3,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.22 (3759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.278

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 17-63919139-C-A is Benign according to our data. Variant chr17-63919139-C-A is described in ClinVar as [Benign]. Clinvar id is 1296769.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 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: 0.219 AC: 33245 AN: 152008 Hom.: 3760 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0570

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.219 AC: 33240 AN: 152124 Hom.: 3759 Cov.: 32 AF XY: 0.213 AC XY: 15811 AN XY: 74364

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0569

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.227

Alfa AF: 0.229 Hom.: 485

Bravo AF: 0.216

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2011732; hg19: chr17-61996499;