rs11882186

chr19-15201219-C-Achr19-15201219-C-Gchr19-15201219-C-T

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 0.193 in 151,520 control chromosomes in the GnomAD database, including 3,628 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3628 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.186

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 19-15201219-C-A is Benign according to our data. Variant chr19-15201219-C-A is described in ClinVar as [Benign]. Clinvar id is 1180159.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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: 0.193 AC: 29229 AN: 151412 Hom.: 3614 Cov.: 30

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.193 AC: 29271 AN: 151520 Hom.: 3628 Cov.: 30 AF XY: 0.191 AC XY: 14129 AN XY: 74006

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.172

Alfa AF: 0.109 Hom.: 300

Bravo AF: 0.211

Asia WGS AF: 0.241 AC: 835 AN: 3472

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

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.4
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11882186; hg19: chr19-15312030;