rs1024611

Positions:

• chr17-34252769-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.287 in 152,162 control chromosomes in the GnomAD database, including 6,922 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,risk factor (no stars).

• Frequency: Genomes: 𝑓 0.29 (6922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Conflicting classifications of pathogenicity; risk factor no assertion criteria provided P:1 B:1 O:3
• Conservation: PhyloP100: -0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.287 AC: 43582 AN: 152044 Hom.: 6908 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.287 AC: 43619 AN: 152162 Hom.: 6922 Cov.: 33 AF XY: 0.296 AC XY: 21990 AN XY: 74382

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.284

Alfa AF: 0.268 Hom.: 529

Bravo AF: 0.290

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity; risk factor

Submissions summary: Pathogenic:1 Benign:1 Other:3

Revision: no assertion criteria provided

Submissions by phenotype

Coronary artery disease, development of, in HIV Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 15, 2009

- -

CCL2-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 10, 2023

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Mycobacterium tuberculosis, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jan 15, 2009

- -

Coronary artery disease, modifier of Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jan 15, 2009

- -

Spina bifida, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jan 15, 2009

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.18
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024611; hg19: chr17-32579788;