rs1524668

Variant names:

• chr2-9557243-A-C
• rs1524668

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 0.63 in 151,838 control chromosomes in the GnomAD database, including 31,513 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: 𝑓 0.63 (31513 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.630 AC: 95527 AN: 151720 Hom.: 31482 Cov.: 30

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.630 AC: 95603 AN: 151838 Hom.: 31513 Cov.: 30 AF XY: 0.615 AC XY: 45581 AN XY: 74132

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.649

Alfa AF: 0.645 Hom.: 11182

Bravo AF: 0.628

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Mycobacterium tuberculosis, susceptibility to Uncertain:1

Dec 12, 2023

Laboratory Of Immunobiology And Genetics, Instituto Nacional De Enfermedades Respiratorias Ismael Cosio Villegas

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524668; hg19: chr2-9697372;