rs17248720

Variant names:

• chr19-11087511-C-T
• rs17248720

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.162 in 151,590 control chromosomes in the GnomAD database, including 2,419 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (2419 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.103
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 19-11087511-C-T is Benign according to our data. Variant chr19-11087511-C-T is described in ClinVar as Benign. ClinVar VariationId is 684564.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 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: 0.162 AC: 24559 AN: 151494 Hom.: 2414 Cov.: 30

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0490

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.162 AC: 24585 AN: 151590 Hom.: 2419 Cov.: 30 AF XY: 0.164 AC XY: 12119 AN XY: 74042

African (AFR) AF: 0.271 AC: 11211 AN: 41294

American (AMR) AF: 0.158 AC: 2395 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3468

East Asian (EAS) AF: 0.0493 AC: 254 AN: 5152

South Asian (SAS) AF: 0.165 AC: 792 AN: 4800

European-Finnish (FIN) AF: 0.115 AC: 1207 AN: 10476

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7790 AN: 67920

Other (OTH) AF: 0.148 AC: 310 AN: 2100

Alfa AF: 0.129 Hom.: 286

Bravo AF: 0.172

Asia WGS AF: 0.143 AC: 501 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypercholesterolemia, familial, 1 Benign:1

Jul 16, 2018

Department of Human Genetics, Laborarztpraxis Dres. Walther, Weindel und Kollegen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Due to the increased occurrence of the mutation (>= 5%), this variant is classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs17248720; hg19: chr19-11198187;