rs1024611

Variant names:

• chr17-34252769-A-G
• rs1024611

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

Jan 15, 2009

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

CCL2-related disorder Benign:1

Jul 10, 2023

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

Jan 15, 2009

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Coronary artery disease, modifier of Other:1

Jan 15, 2009

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Spina bifida, susceptibility to Other:1

Jan 15, 2009

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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;